Systems and methods for multiplex analysis of PCR in real time

ABSTRACT

The present invention provides methods and systems for real-time measurements of PCR with multiplexing capability. Certain embodiments relate to methods and systems that use fluorescently encoded superparamagnetic microspheres for the immobilization of amplification products during the PCR process, and an imaging chamber of a measurement device that is also capable of controllable thermal cycling for assisting the PCR process.

This application claims priority to U.S. provisional patent application60/869,742, filed Dec. 13, 2006, the entire disclosure of which isincorporated by reference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

This invention generally relates to systems and methods for performingmeasurements of DNA amplification such as PCR. In particular, thisinvention relates to “real time” measurements of PCR with multiplexingcapability. Certain embodiments relate to a system which uses particles,such as paramagnetic microspheres, and an imaging chamber of ameasurement device which is also capable of controllable thermal cyclingfor assisting the PCR process.

2. Description of Related Art

Polymerase chain reaction (PCR) is a molecular biology technique forenzymatically replicating DNA without using a living organism. PCR iscommonly used in medical and biological research labs for a variety oftasks, such as the detection of hereditary diseases, the identificationof genetic fingerprints, the diagnosis of infectious diseases, thecloning of genes, paternity testing, and DNA computing. PCR has beenaccepted by molecular biologists as the method of choice for nucleicacid detection because of its unparalleled amplification and precisioncapability. DNA detection is typically performed at the end-point, orplateau phase of the PCR reaction, making it difficult to quantify thestarting template. Real-time PCR or kinetic PCR advances the capabilityof end-point PCR analysis by recording the amplicon concentration as thereaction progresses. Amplicon concentration is most often recorded via afluorescent signal change associated with the amplified target.Real-time PCR is also advantageous over end-point detection in thatcontamination is limited because it can be performed in a closed system.Other advantages include greater sensitivity, dynamic range, speed, andfewer processes required.

Several assay chemistries have been used in real-time PCR detectionmethods. These assay chemistries include using double-stranded DNAbinding dyes, dual-labeled oligonucleotides, such as hairpin primers,and hairpin probes. Other chemistries include exonuclease based probessuch as hydrolysis probes. Various PCR and real-time PCR methods aredisclosed in U.S. Pat. Nos. 5,656,493; 5,994,056; 6,174,670; 5,716,784;6,030,787; and 6,174,670, which are incorporated herein by reference.

A drawback of current real-time PCR is its limited multiplexingcapability. Current real-time PCR technologies use reporterfluorochromes that are free in solution. This design necessitates theuse of spectrally distinct fluorochromes for each assay within amultiplex reaction. For example, a multiplex reaction designed to detect4 target sequences would require an instrument capable of distinguishing4 different free floating fluorochromes by spectral differentiation, notincluding controls. These requirements not only limit the practicalmultiplexing capability, but also increase costs since such instrumentstypically require multiple lasers and filters. Current real-time PCRtechnologies have multiplexing capabilities from about 1-6 plex.

SUMMARY OF THE INVENTION

The present invention relates to systems and methods for amplificationand detection of DNA. In particular, the present invention providessystems and methods that greatly increase multiplexing capabilities ofreal-time PCR. In one embodiment, the present invention provides amethod of amplifying and detecting a plurality of nucleic acid targetsin a sample comprising: (a) combining in a chamber a sample comprisingthe plurality of nucleic acid targets, a plurality of primer pairs forpriming amplification of the plurality of nucleic acid targets, alabeling agent, and a plurality of probes complementary to the pluralityof nucleic acid targets, wherein the probes are immobilized on aplurality of encoded particles such that the identity of each probe isknown from the encoded particle on which it is immobilized; (b)performing an amplification cycle to form amplification products foreach of the plurality of nucleic acid targets amplified with theplurality of primer pairs; (c) hybridizing the amplification products tothe probes immobilized on the encoded particles; (d) attracting theencoded particles and the amplification products hybridized to theprobes immobilized on the encoded particles to the surface of thechamber; (e) detecting a signal from the encoded particles and detectinga signal directly (e.g., a label incorporated into the amplificationproduct) or indirectly (e.g., a labeled complementary nucleic acidsequence hybridized to the amplification product) from the amplificationproducts; (f) dispersing the encoded particles and the amplificationproducts hybridized to the probes immobilized on the encoded particlesfrom the surface of the chamber prior to performing a furtheramplification cycle; and (g) repeating steps (b) through (f) at leastonce; wherein the plurality of nucleic acid targets in the sample areamplified and detected. In certain aspects of the invention, steps (b)through (f) are repeated between 10 to 40 times.

The particles may be particles with magnetic properties and/or particleswith a density that allows them to rest upon a two dimensional surfacein solution. The particles may in one way or another rest upon a twodimensional surface by magnetic, gravitational, or ionic forces, or bychemical bonding, or by any other means known to those skilled in theart. Particles may consist of glass, polystyrene, latex, metal, quantumdot, polymers, silica, metal oxides, ceramics, or any other substancesuitable for binding to nucleic acids, or chemicals or proteins whichcan then attach to nucleic acids. The particles may be rod shaped orspherical or disc shaped, or comprise any other shape. The particles mayalso be distinguishable by their shape or size or physical location. Theparticles may be spectrally distinct by virtue of having a compositioncontaining dyes or ratios or concentrations of one or more dyes orfluorochromes, or may be distinguishable by barcode or holographicimages or other imprinted forms of particle coding. Where the particlesare magnetic particles, they may be attracted to the surface of thechamber by application of a magnetic field. Likewise, magnetic particlesmay be dispersed from the surface of the chamber by removal of themagnetic field. The magnetic particles are preferably paramagnetic orsuperparamagnetic. Paramagnetic and superparamagnetic particles havenegligible magnetism in the absence of a magnetic field, but applicationof a magnetic field induces alignment of the magnetic domains in theparticles, resulting in attraction of the particles to the field source.When the field is removed, the magnetic domains return to a randomorientation so there is no interparticle magnetic attraction orrepulsion. In the case of superparamagnetism, this return to randomorientation of the domains is nearly instantaneous, while paramagneticmaterials will retain domain alignment for some period of time afterremoval of the magnetic field. Where the particles have a sufficientdensity they may be attracted to the bottom surface of the chamber bygravity, and dispersed from the bottom surface of the chamber byagitation of the chamber, such as by vortexing, sonication, or fluidicmovement. Agitation of the chamber may also be used to further assist indispersing particles in methods and systems in which the particles wereattracted to a surface of the chamber by other forces, such as magneticor ionic forces, or suction forces, or vacuum filtration, or affinity,or hydrophilicity or hydrophobicity, or any combination thereof.

In one embodiment, the present invention provides a method of amplifyingand detecting a plurality of nucleic acid targets in a samplecomprising: (a) combining in a chamber a sample comprising the pluralityof nucleic acid targets, a plurality of primer pairs for primingamplification of the plurality of nucleic acid targets, a labelingagent, and a plurality of probes complementary to the plurality ofnucleic acid targets, wherein the probes are immobilized on a pluralityof encoded magnetic beads such that the identity of each probe is knownfrom the encoded magnetic bead on which it is immobilized; (b)performing an amplification cycle to form labeled amplification productsfor each of the plurality of nucleic acid targets amplified with theplurality of primer pairs; (c) hybridizing the labeled amplificationproducts to the probes immobilized on the encoded magnetic beads; (d)applying a magnetic field to a surface of the chamber to draw theencoded magnetic beads and the labeled amplification products hybridizedto the probes immobilized on the encoded magnetic beads to the surfaceof the chamber; (e) detecting the encoded magnetic beads and the labeledamplification products; (f) removing the magnetic field from the surfaceof the chamber prior to performing a further amplification cycle; and(g) repeating steps (b) through (f) at least once; wherein the pluralityof nucleic acid targets in the sample are amplified and detected. Incertain aspects of the invention, steps (b) through (f) are repeatedbetween 10 to 40 times.

A labeling agent, which may also be referred to as a reporter, is amolecule that facilitates the detection of a molecule (e.g., a nucleicacid sequence) to which it is attached. Numerous reporter molecules thatmay be used to label nucleic acids are known. Direct reporter moleculesinclude fluorophores, chromophores, and radiophores. Non-limitingexamples of fluorophores include, a red fluorescent squarine dye such as2,4-Bis[1,3,3-trimethyl-2-indolinylidenemethyl]cyclobutenediylium-1,3-dioxolate,an infrared dye such as 2,4Bis[3,3-dimethyl-2-(1H-benz[e]indolinylidenemethyl)]cyclobutenediylium-1,3-dioxolate,or an orange fluorescent squarine dye such as2,4-Bis[3,5-dimethyl-2-pyrrolyl]cyclobutenediylium-1,3-diololate.Additional non-limiting examples of fluorophores include quantum dots,Alexa Fluor® dyes, AMCA, BODIPY® 630/650, BODIPY® 650/665, BODIPY®-FL,BODIPY®-R6G, BODIPY®-TMR, BODIPY®-TRX, Cascade Blue®, CyDye™, includingbut not limited to Cy2™, Cy3™, and Cy5™, a DNA intercalating dye,6-FAM™, Fluorescein, HEX™, 6-JOE, Oregon Green® 488, Oregon Green® 500,Oregon Green® 514, Pacific Blue™, REG, phycobilliproteins including, butnot limited to, phycoerythrin and allophycocyanin, Rhodamine Green™,Rhodamine Red™, ROX™, TAMRA™, TET™, Tetramethylrhodamine, or Texas Red®.A signal amplification reagent, such as tyramide (PerkinElmer), may beused to enhance the fluorescence signal. Indirect reporter moleculesinclude biotin, which must be bound to another molecule such asstreptavidin-phycoerythrin for detection. Pairs of labels, such asfluorescence resonance energy transfer pairs or dye-quencher pairs, mayalso be employed.

Labeled amplification products may be labeled directly or indirectly.Direct labeling may be achieved by, for example, using labeled primers,using labeled dNTPs, using labeled nucleic acid intercalating agents, orcombinations of the above. Indirect labeling may be achieved by, forexample, hybridizing a labeled probe to the amplification product.

Encoded particles, such as encoded magnetic beads, may be encoded withfluorescent dyes. Encoding with fluorescent dyes may employ fluorescentdyes with different fluorescent emission wavelengths and/or differentfluorescent intensities.

In another embodiment, the present invention provides a method ofamplifying and detecting a plurality of nucleic acid targets in a samplecomprising: (a) combining in a chamber a sample comprising the pluralityof nucleic acid targets, a plurality of primer pairs for primingamplification of the plurality of nucleic acid targets, wherein oneprimer of each primer pair is labeled, and a plurality of probescomplementary to the plurality of nucleic acid targets, wherein theprobes are immobilized on a plurality of encoded magnetic beads suchthat the identity of each probe is known from the encoded magnetic beadon which it is immobilized; (b) performing an amplification cycle toform labeled amplification products for each of the plurality of nucleicacid targets amplified with the plurality of primer pairs; (c)hybridizing the labeled amplification products to the probes immobilizedon the encoded magnetic beads; (d) applying a magnetic field to asurface of the chamber to draw the encoded magnetic beads and thelabeled amplification products hybridized to the probes immobilized onthe encoded magnetic beads to the surface of the chamber; (e) detectingthe encoded magnetic beads and the labeled amplification products; (f)removing the magnetic field from the surface of the chamber prior toperforming a further amplification cycle; and (g) repeating steps (b)through (f) at least once; wherein the plurality of nucleic acid targetsin the sample are amplified and detected. In certain aspects of theinvention, steps (b) through (f) are repeated between 10 to 40 times.

In yet another embodiment, the present invention provides a method ofamplifying and detecting a plurality of nucleic acid targets in a samplecomprising: (a) combining in a chamber a sample comprising the pluralityof nucleic acid targets, a plurality of primer pairs for primingamplification of the plurality of nucleic acid targets, and a pluralityof molecular beacons complementary to the plurality of nucleic acidtargets, wherein the molecular beacons are immobilized on a plurality ofencoded magnetic beads such that the identity of each molecular beaconis known from the encoded magnetic bead on which it is immobilized; (b)performing an amplification cycle to form amplification products foreach of the plurality of nucleic acid targets amplified with theplurality of primer pairs; (c) hybridizing the amplification products tothe molecular beacons immobilized on the encoded magnetic beads; (d)applying a magnetic field to a surface of the chamber to draw theencoded magnetic beads and the amplification products hybridized to themolecular beacons immobilized on the encoded magnetic beads to thesurface of the chamber; (e) detecting a signal from the encoded magneticbeads and a signal from the molecular beacons; (f) removing the magneticfield from the surface of the chamber prior to performing a furtheramplification cycle; and (g) repeating steps (b) through (f) at leastonce; wherein the plurality of nucleic acid targets in the sample areamplified and detected. In certain aspects of the invention, steps (b)through (f) are repeated between 10 to 40 times.

In one embodiment, the present invention provides a method of amplifyingand detecting a plurality of nucleic acid targets in a samplecomprising: (a) combining in a chamber a sample comprising the pluralityof nucleic acid targets, a plurality of primer pairs for primingamplification of the plurality of nucleic acid targets, and a pluralityof probe sets complementary to the plurality of nucleic acid targets,wherein each probe set comprises a first probe labeled with a firstmember of a fluorescent energy transfer pair and immobilized on anencoded magnetic bead such that the identity of the first probe is knownfrom the encoded magnetic bead on which it is immobilized, and a secondprobe with a second member of the fluorescent energy transfer pair; (b)performing an amplification cycle to form amplification products foreach of the plurality of nucleic acid targets amplified with theplurality of primer pairs; (c) hybridizing the amplification products tothe probe sets; (d) applying a magnetic field to a surface of thechamber to draw the encoded magnetic beads and the amplificationproducts hybridized to the probes immobilized on the encoded magneticbeads to the surface of the chamber; (e) detecting a signal from theencoded magnetic beads and a signal from the fluorescent energy transferpair hybridized to the amplification products; (f) removing the magneticfield from the surface of the chamber prior to performing a furtheramplification cycle; and (g) repeating steps (b) through (f) at leastonce; wherein the plurality of nucleic acid targets in the sample areamplified and detected. In certain aspects of the invention, steps (b)through (f) are repeated between 10 to 40 times. In certain aspects, thesignal from the fluorescent energy transfer pair is an increase influorescence. In other aspects, the signal from the fluorescent energytransfer pair is a decrease in fluorescence.

In another embodiment, the present invention provides a method ofamplifying and detecting a nucleic acid target in a sample comprising:(a) combining in a chamber a sample comprising the nucleic acid target,a primer pair for priming amplification of the nucleic acid target, anda probe set complementary to the nucleic acid target, wherein the probeset comprises a first probe immobilized on a magnetic bead, and a secondprobe comprising a label; (b) performing an amplification cycle to formamplification products for the nucleic acid target amplified with theprimer pair; (c) hybridizing the amplification products to the probeset; (d) applying a magnetic field to a surface of the chamber to drawthe magnetic bead and the amplification products hybridized to the probeimmobilized on the encoded magnetic bead to the surface of the chamber;(e) detecting a signal from the second probe hybridized to theamplification products; (f) removing the magnetic field from the surfaceof the chamber prior to performing a further amplification cycle; and(g) repeating steps (b) through (f) at least once; wherein the nucleicacid target in the sample is amplified and detected. This method may beperformed as a single-plex or multi-plex. Multi-plexing may be achievedby using different labels on the second probes and/or by labeling orencoding the particles on which the first probes are immobilized.

In another embodiment, the present invention provides a method ofamplifying and detecting a nucleic acid target in a sample comprising:(a) combining in a chamber a sample comprising the nucleic acid target,a primer pair for priming amplification of the nucleic acid target, adNTP coupled to a quencher molecule, and a fluorescently labeled probecomplementary to the nucleic acid target, wherein the probe isimmobilized on a magnetic beads; (b) performing an amplification cycleto form amplification products of the nucleic acid target, theamplification products comprising quencher molecules; (c) hybridizingthe amplification products to the probe immobilized on the magneticbead; (d) applying a magnetic field to a surface of the chamber to drawthe magnetic bead and the amplification products hybridized to the probeimmobilized on the encoded magnetic bead to the surface of the chamber;(e) detecting a signal from the labeled probe, wherein a decrease in thesignal from the labeled probe indicates hybridization of the labeledprobe to the amplification products comprising quencher molecules; (f)removing the magnetic field from the surface of the chamber prior toperforming a further amplification cycle; and (g) repeating steps (b)through (f) at least once; wherein the nucleic acid target in the sampleis amplified and detected. This method may be performed as a single-plexor multi-plex. Multi-plexing may be achieved by using different labelson the probes and/or by labeling or encoding the particles on which theprobes are immobilized.

In another embodiment, the present invention provides a method ofamplifying and detecting a plurality of nucleic acid targets in a samplecomprising: (a) combining in a chamber a sample comprising the pluralityof nucleic acid targets, a plurality of primer pairs for primingamplification of the plurality of nucleic acid targets, and a pluralityof probe sets complementary to the plurality of nucleic acid targets,wherein each probe set comprises a first probe immobilized on an encodedmagnetic bead such that the identity of the first probe is known fromthe encoded magnetic bead on which it is immobilized, and a second probecomprising a label; (b) performing an amplification cycle to formamplification products for each of the plurality of nucleic acid targetsamplified with the plurality of primer pairs; (c) hybridizing theamplification products to the probe sets; (d) applying a magnetic fieldto a surface of the chamber to draw the encoded magnetic beads and theamplification products hybridized to the probes immobilized on theencoded magnetic beads to the surface of the chamber; (e) detecting asignal from the encoded magnetic beads and a signal from the secondprobe hybridized to the amplification products; (f) removing themagnetic field from the surface of the chamber prior to performing afurther amplification cycle; and (g) repeating steps (b) through (f) atleast once; wherein the plurality of nucleic acid targets in the sampleare amplified and detected. In certain aspects of the invention, steps(b) through (f) are repeated between 10 to 40 times.

In a further embodiment, the present invention provides a method ofamplifying and detecting a plurality of nucleic acid targets in a samplecomprising: (a) combining in a chamber a sample comprising the pluralityof nucleic acid targets, a plurality of primer pairs for primingamplification of the plurality of nucleic acid targets, a dNTP coupledto a quencher molecule, and a plurality of fluorescently labeled probescomplementary to the plurality of nucleic acid targets, wherein theprobes are immobilized on a plurality of encoded magnetic beads suchthat the identity of each probe is known from the encoded magnetic beadon which it is immobilized; (b) performing an amplification cycle toform amplification products comprising quencher molecules for each ofthe plurality of nucleic acid targets amplified with the plurality ofprimer pairs; (c) hybridizing the amplification products to the probesimmobilized on the encoded magnetic beads; (d) applying a magnetic fieldto a surface of the chamber to draw the encoded magnetic beads and theamplification products hybridized to the probes immobilized on theencoded magnetic beads to the surface of the chamber; (e) detecting asignal from the encoded magnetic beads and a signal from the labeledprobes, wherein a decrease in the signal from the labeled probesindicates hybridization of the labeled probes to the amplificationproducts comprising quencher molecules; (f) removing the magnetic fieldfrom the surface of the chamber prior to performing a furtheramplification cycle; and (g) repeating steps (b) through (f) at leastonce; wherein the plurality of nucleic acid targets in the sample areamplified and detected. In certain aspects of the invention, steps (b)through (f) are repeated between 10 to 40 times.

In another embodiment, the present invention provides a method ofamplifying and detecting a plurality of nucleic acid targets in a samplecomprising: (a) combining in a chamber a sample comprising the pluralityof nucleic acid targets; a plurality of primer pairs for primingamplification of the plurality of nucleic acid targets, wherein eachprimer pair comprises a first primer comprising a target specificsequence, a tag sequence 5′ of the target specific sequence, andoptionally a blocker between the target specific sequence and the tagsequence, and a second primer comprising a target specific sequence; alabeling agent; and a plurality of probes complementary to the tagsequences of the plurality of primer pairs, wherein the probes areimmobilized on a plurality of encoded magnetic beads such that theidentity of each probe is known from the encoded magnetic bead on whichit is immobilized; (b) performing an amplification cycle to form taggedand labeled amplification products for each of the plurality of nucleicacid targets amplified with the plurality of primer pairs; (c)hybridizing the tagged and labeled amplification products to the probesimmobilized on the encoded magnetic beads; (d) applying a magnetic fieldto a surface of the chamber to draw the encoded magnetic beads and thetagged and labeled amplification products hybridized to the probesimmobilized on the encoded magnetic beads to the surface of the chamber;(e) detecting the encoded magnetic beads and the tagged and labeledamplification products; (f) removing the magnetic field from the surfaceof the chamber prior to performing a further amplification cycle; and(g) repeating steps (b) through (f) at least once; wherein the pluralityof nucleic acid targets in the sample are amplified and detected. Incertain aspects of the invention, steps (b) through (f) are repeatedbetween 10 to 40 times. In certain aspects, the labeling agent is areporter molecule attached to the second primer of the primer pair. Inother aspects, the labeling agent is a nucleic acid intercalating dye.It should be noted that the nucleic acid intercalating agent will labelthe hybridized complementary tags even in the absence of amplification.This would be problematic in PCR where only an end-point detection isperformed because it would be unclear whether amplification wassuccessful or whether the detected signal was only from theintercalating agent labeling the complementary tags. With PCR performedin real time according to the methods disclosed herein, the signal fromthe intercalating agent would be observed to increase as the number ofamplification cycles increased in a successful amplification. Thusallowing the differentiation between successful amplification and thelabeling only of the complementary tags.

The methods disclosed herein may further comprise quantifying theinitial amount of the nucleic acid target(s) in the sample. Thequantification may comprise, for example, determining the relativeconcentrations of DNA present during the exponential phase of thereal-time PCR by plotting fluorescence against cycle number on alogarithmic scale. The amounts of DNA may then be determined bycomparing the results to a standard curve produced by real-time PCR ofserial dilutions of a known amount of DNA. Additionally, real-time PCRmay be combined with reverse transcription polymerase chain reaction toquantify RNAs in a sample, including low abundance RNAs.

The methods disclosed herein provide multiplexing capabilities such thata plurality of primer pairs may amplify a plurality of target nucleicacids in a single PCR reaction. In certain embodiments there are atleast 6, 7, 8, 9, 10, 11, or 12 different primer pairs in a PCRreaction. In some embodiments there are between 8 to 100, 8 to 80, 8 to60, 8 to 40, 8 to 20, 8 to 18, 8 to 16, 8 to 12, 10 to 100, 10 to 80, 10to 60, 10 to 40, 10 to 20, 10 to 18, 10 to 16, 10 to 12, 12 to 100, 12to 80, 12 to 60, 12 to 40, 12 to 20, 12 to 18, or 12 to 16 differentprimer pairs in a PCR reaction. In certain embodiments there are atleast 6, 7, 8, 9, 10, 11, or 12 different target nucleic acids in a PCRreaction. In some embodiments there are between 8 to 100, 8 to 80, 8 to60, 8 to 40, 8 to 20, 8 to 18, 8 to 16, 8 to 12, 10 to 100, 10 to 80, 10to 60, 10 to 40, 10 to 20, 10 to 18, 10 to 16, 10 to 12, 12 to 100, 12to 80, 12 to 60, 12 to 40, 12 to 20, 12 to 18, or 12 to 16 differenttarget nucleic acids in a PCR reaction. Probes present in the PCRreaction may comprise a blocked 3′ hydroxyl group to prevent extensionof the probes by the polymerase. The 3′ hydroxyl group may be blockedwith, for example, a phosphate group or a 3′ inverted dT.

The target nucleic acid sequence may be any sequence of interest. Thesample containing the target nucleic acid sequence may be any samplethat contains nucleic acids. In certain aspects of the invention thesample is, for example, a subject who is being screened for the presenceor absence of one or more genetic mutations or polymorphisms. In anotheraspect of the invention the sample may be from a subject who is beingtested for the presence or absence of a pathogen. Where the sample isobtained from a subject, it may be obtained by methods known to those inthe art such as aspiration, biopsy, swabbing, venipuncture, spinal tap,fecal sample, or urine sample. In some aspects of the invention, thesample is an environmental sample such as a water, soil, or air sample.In other aspects of the invention, the sample is from a plant, bacteria,virus, fungi, protozoan, or metazoan.

Each amplification cycle has three phases: a denaturing phase, a primerannealing phase, and a primer extension phase. The amplification cyclecan be repeated until the desired amount of amplification product isproduced. Typically, the amplification cycle is repeated between about10 to 40 times. For real-time PCR, detection of the amplificationproducts will typically be done after each amplification cycle. Althoughin certain aspects of the invention, detection of the amplificationproducts may be done after every second, third, fourth, or fifthamplification cycle. Detection may also be done such that as few as 2 ormore amplification cycles are analyzed or detected. The amplificationcycle may be performed in the same chamber in which the detection of theamplification occurs, in which case this chamber would need to comprisea heating element so the temperature in the chamber can be adjusted forthe denaturing phase, primer annealing phase, and a primer extensionphase of the amplification cycle. The heating element would typically beunder the control of a processor. The amplification cycle may, however,be performed in a different chamber from the chamber in which detectionof the amplification occurs, in which case the “amplification” chamberwould need to comprise a heating element but the “detection” or“imaging” chamber would not be required to have a heating element. Whereamplification and detection occur in separate chambers, the fluid inwhich the amplification reaction occurs may be transferred between thechambers by, for example, a pump or piston. The pump or piston may beunder the control of a processor. Alternatively, the fluid may betransferred between the chambers manually using, for example, a pipette.

The chamber may be for example, a quartz chamber. A magnetic field maybe applied to the chamber to attract magnetic particles within thechamber to a surface of the chamber by placing a permanent magnetadjacent to the surface of the chamber or by turning on an electromagnetadjacent to the surface of the chamber. The magnet need not be inphysical contact with the chamber as long as it is close enough for itsmagnetic field to attract the magnetic particles within the chamber tothe chamber surface. The magnetic field may be removed from the chamberby moving the permanent magnet away from the chamber or by turning offthe electromagnetic. Of course, an electromagnet that is turned on mayalso be applied or removed from the chamber by moving closer or fartherfrom the chamber as described above for a permanent magnet. Inembodiments where the amplification and detection occur in the samechamber, the magnetic field may be applied during the primer annealingphase of the amplification cycle, during the primer extension phase ofthe amplification cycle, or following the amplification cycle. Inembodiments, where the amplification and detection occur in differentchambers, the magnetic field will typically be applied following theamplification cycle when the amplification reaction fluid is transferredinto the detection chamber.

The encoded particles and amplification products on the surface of thechamber may be detected using an imaging system such as those describedherein. For example, detecting the encoded magnetic beads and thelabeled amplification products may comprise imaging fluorescentwavelengths and/or fluorescent intensities emitted from the encodedmagnetic beads and the labeled amplification products. The imaging maycomprise taking a decoding image to identify the beads on the surface ofthe chamber and taking an assay imaging to detect amplification productson the surface of the chamber. A comparison of the decoding image andthe assay image shows which beads have amplification products bound tothem. Since the identities of the probes attached to the beads is knownby encoding of the beads, the identity of the amplification producthybridized to the probe may also be determined. The methods of thepresent invention may further comprise correlating the signal from thedirectly or indirectly labeled amplification product with theconcentration of DNA or RNA in a sample. This correlation may comprisethe steps of determining the relative concentrations of DNA presentduring the exponential phase of real-time PCR by plotting fluorescenceagainst cycle number on a logarithmic scale and comparing the results toa standard curve produced by real-time PCR of serial dilutions of aknown amount of DNA or RNA.

In one embodiment, the present invention provides a system forperforming multiplexed, real-time PCR comprising: a thermal cycler; animaging system coupled to the thermal cycler; encoded magnetic particlesadapted to be introduced into the thermal cycler; a magnet forselectively introducing a magnetic field to the thermal cycler forimmobilizing the encoded magnetic particles.

It is contemplated that any method or composition described herein canbe implemented with respect to any other method or composition describedherein.

The use of the term “or” in the claims is used to mean “and/or” unlessexplicitly indicated to refer to alternatives only or the alternativesare mutually exclusive, although the disclosure supports a definitionthat refers to only alternatives and “and/or.”

Throughout this application, the term “about” is used to indicate that avalue includes the standard deviation of error for the device or methodbeing employed to determine the value.

Following long-standing patent law, the words “a” and “an,” when used inconjunction with the word “comprising” in the claims or specification,denotes one or more, unless specifically noted.

Other objects, features and advantages of the present invention willbecome apparent from the following detailed description. It should beunderstood, however, that the detailed description and the specificexamples, while indicating specific embodiments of the invention, aregiven by way of illustration only, since various changes andmodifications within the spirit and scope of the invention will becomeapparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and areincluded to further demonstrate certain aspects of the presentinvention. The invention may be better understood by reference to one ormore of these drawings in combination with the detailed description ofspecific embodiments presented herein.

FIG. 1 is a schematic drawing of an imaging system.

FIG. 2 is a block diagram showing functional details of the system shownin FIG. 1.

FIG. 3 is a schematic diagram illustrating the relation of microspheresin a detection chamber.

FIG. 4 is another schematic diagram illustrating the relation ofmicrospheres in a detection chamber.

FIG. 5 is an illustration of molecular beacon probes in their hairpinconformation and in their open conformation when hybridized to acomplementary nucleic acid sequence.

FIG. 6 is an illustration of molecular beacon probes in their openconformation when hybridized to a complementary nucleic acid sequence.Positioning of the magnet in proximity to the imaging chamber results inthe molecular beacon probes being immobilized on the surface of theimaging chamber because they are attached to magnetically responsivemicrospheres.

FIG. 7 illustrates a FRET detection chemistry.

FIG. 8 illustrates a detection chemistry in which quenching moleculesare incorporated into a newly synthesized DNA strand and a complementaryprobe is labeled with a fluorochrome attached to the surface of a bead.

FIG. 9 is a block diagram of an imaging system.

FIG. 10 is a block diagram of a flow cytometer used as an imagingsystem.

FIG. 11 illustrates a direct hybridization detection chemistry in whichone primer of a primer pair is labeled at its 5′ end with a reportermolecule.

FIG. 12 illustrates a two probe detection chemistry.

FIG. 13 shows the Factor V Leiden genomic gene sequence (SEQ ID NO: 6and 7).

FIG. 14 is a graph of Median Fluorescent Intensity (MFI) (y-axis) andcycle number (x-axis) during PCR.

FIG. 15 shows various Cystic Fibrosis gene sequences (SEQ ID NO: 8-15).

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

A. Imaging Systems

Turning now to the drawings, it is noted that the figures are not drawnto scale. In particular, the scale of some of the elements of thefigures is greatly exaggerated to emphasize characteristics of theelements. It is also noted that the figures are not drawn to the samescale. Elements shown in more than one figure that may be similarlyconfigured have been indicated using the same reference numerals.

The embodiments of the imaging system of FIGS. 1, 2, and 9 includeseveral configurations using two broad based imaging methods. Forfluorescence detection, a single sensor such as a photomultiplier tube(PMT) or avalanche photodiode (APD) per detected wavelength may beemployed. Alternatively, a one- or two-dimensional charge coupled device(CCD) or another suitable array detector may be used for fluorescencedetection. The excitation source may be configured to provide widespreadillumination (i.e., illumination provided over a relatively large areaof the imaging volume of the measurement device (such as the entireimaging volume of the measurement device) simultaneously) using lightemitted by light sources such as light emitting diodes (LEDs) anddelivered to one or more materials in the imaging volume of themeasurement device directly or via fiber optics. Alternatively, theexcitation source may be configured to provide illumination of arelatively small spot in the imaging volume of the measurement device,and the system may be configured to scan the relatively small spotacross the imaging volume. In this manner, the illumination may beconfigured as a relatively “tiny flying spot” of focused light generatedfrom one or more LEDs, one or more lasers, one or more other suitablelight sources, or some combination thereof.

FIGS. 1 and 2 illustrate one embodiment of a system configured to imageone or more materials in an imaging volume of a measurement device. Thissystem embodiment includes detectors 34, 36, and 38. Detectors 34, 36,and 38 may be CCD cameras or any other suitable imaging devices. Each ofthe detectors may have the same configuration or differentconfigurations. Each of the detectors may be configured to detect light(e.g., light fluoresced from particles 40 in imaging volume defined byimaging or detection chamber 42) at a different wavelength or wavelengthband. In addition, each of the detectors may be configured to generateimages or “capture fluorescent pictures” of particles 40 in imagingchamber 42 (e.g., particles at the bottom of imaging chamber 42).

In FIGS. 1 and 2, the microspheres 40 are fed into the imaging chamberwhich may be coupled to a thermal cycling element (not shown), suchthat, the microspheres are contained in the same solution as the PCRreaction, during the PCR reaction. Microspheres 40 may be pulled to asurface of imaging chamber 42 at any phase of the PCR cycle by applyinga magnetic field with a magnet 264. Microspheres 40 may be released fromthe surface by removing the magnetic field. During the next detectionphase, the microspheres will again be pulled to the surface for imaging.In FIGS. 1 and 2, the microspheres 40 may also be fed directly to theimaging chamber 42 from a thermal cycler (not shown). Microspheres 40may be introduced to the imaging chamber 42 and pulled to a surface atany phase of the PCR cycle.

FIGS. 1 and 2 illustrate a magnet 264 for selectively pulling themagnetic microspheres 40 to a surface. The system of FIGS. 1 and 2 alsoincludes light sources 44 and 46 configured to emit light havingdifferent wavelengths or different wavelength bands (e.g., one of thelight sources may be configured to emit red light and the other lightsource may be configured to emit green light). The light emitted bylight sources 44 and 46 may include, for example, light in any part ofthe visible wavelength regime. Light sources 44 and 46 may include LEDsor any other suitable light sources known in the art. Light sources 44and 46 are arranged above the periphery of imaging chamber 42. Inaddition, the light sources are arranged above the imaging chamber suchthat each light source directs light to particles 40 in imaging chamber42 at different directions. The system also includes filters 48 and 50coupled to light sources 44 and 46, respectfully. Filters 48 and 50 maybe bandpass filters or any other suitable spectral filters known in theart. In this manner, the system may use light sources 44 and 46 andfilters 48 and 50 to sequentially illuminate the particles withdifferent wavelengths or different wavelength bands of light. Forexample, red light may be used to excite classification dyes (not shown)that may be internal to the particles, and green light may be used toexcite reporter molecules (not shown) coupled to the surface of theparticles. Since the classification illumination is dark during reportermeasurements (i.e., in the above example, red light is not directed tothe particles while green light is directed to the particles), theanalyte measurement sensitivity of the system will not be reduced due tocrosstalk from out of band light.

The system may also include single lens 52 positioned at the center (orapproximately the center) of the illumination “ring.” Lens 52 mayinclude any suitable refractive optical element known in the art. Lens52 is configured to image light scattered and/or fluoresced from theparticles onto one or more monochrome CCD detector(s) (e.g., detectors34, 36, and 38) via one or more optical elements, which may include oneor more dichroic and one or more optical bandpass filters. For example,light exiting lens 52 is directed to dichroic filter 54, which mayinclude any suitable dichroic optical element known in the art. Dichroicfilter 54 is configured to reflect light of one wavelength or wavelengthband and to transmit light of other wavelengths or wavelength bands.Light reflected by dichroic filter 54 is directed to filter 56, whichmay be a bandpass filter or other suitable spectral filter. Lightexiting filter 56 is directed to detector 34. Light transmitted bydichroic filter 54 is directed to dichroic filter 58, which may includeany suitable dichroic optical element known in the art. Dichroic filter58 may be configured to reflect light of one wavelength or wavelengthband and to transmit light of other wavelengths or wavelength bands.Light transmitted by dichroic filter 58 is directed to filter 60, whichmay be a bandpass filter or other suitable spectral filter. Lightexiting filter 60 is directed to detector 36. Light reflected bydichroic filter 58 is directed to filter 62, which may be a bandpassfilter or other suitable spectral filter. Light exiting filter 62 isdirected to detector 38.

Furthermore, although the system shown in FIGS. 1 and 2 includes twolight sources, it is to be understood that the system may include anysuitable number of light sources. For example, the system may includemultiple light sources arranged around the periphery of lens 52. In thismanner, light sources may be configured to provide an illumination“ring” surrounding lens 52. Although the system shown in FIGS. 1 and 2includes three detectors configured to image light scattered and/orfluoresced from the particles at different wavelengths or wavelengthbands, it is to be understood that the system may include two or moredetectors. For example, the system may include two or more CCD detectors(and optionally fixed filters) that can be used to simultaneouslymeasure the classification channel(s) and reporter channel(s) therebyproviding higher throughput for the measurements along with additionalhardware cost.

The imaging system may further comprise a fluid handling subsystem fortransferring fluids (e.g., PCR reaction, wash buffers) into thedetection chamber from a storage vessel or from a thermal cycler orother heated chamber if the detection chamber is not capable of thermalcycling. The storage vessel may be configured as a centrifuge tube,injection syringe, micro titer plate or any other suitable samplecontainer known in the art.

The fluid handling subsystem also includes a pump configured to movefluid from the storage vessel, thermal cycler, or other heated chamberto the detection chamber. The pump may have any suitable configurationknown in the art. The fluid handling system may also include one or morevalves configured to control the flow of fluid through the system. Thefluid handling subsystem may also include a wash reservoir for storingfresh water (or other suitable reagent), which may be transferred by thepump to the detection chamber. The pump may also be configured totransfer materials and any other fluid in the detection chamber to awaste vessel. The waste vessel may have any suitable configuration knownin the art. The pumps and valves of the fluid handling subsystem may becontrolled by a processor or operated manually.

The system shown in FIGS. 1 and 2 is, therefore, configured to generatea plurality or series of images representing the fluorescent emission ofparticles 40 at several wavelengths of interest. In addition, the systemmay be configured to supply a plurality or series of digital imagesrepresenting the fluorescence emission of the particles to a processor(i.e., a processing engine). The system may or may not include aprocessor (see e.g. FIG. 9). The processor may be configured to acquire(e.g., receive) image data from detectors 34, 36, and 38. For example,the processor may be coupled to detectors 34, 36, and 38 in any suitablemanner known in the art (e.g., via transmission media (not shown), eachcoupling one of the detectors to the processor, via one or moreelectronic components (not shown) such as analog-to-digital converters,each coupled between one of the detectors and the processor, etc.).Preferably, the processor is configured to process and analyze theseimages to determine one or more characteristics of particles 40 such asa classification of the particles and information about an analyte onthe surface of the particles. The one or more characteristics may beoutput by the processor in any suitable format such as a data array withan entry for fluorescent magnitude for each particle for eachwavelength. Specifically, the processor may be configured to perform oneor more steps of a method for processing and analyzing the images.Examples of methods for processing and analyzing images generated by asystem such as that shown in FIGS. 1 and 2 are illustrated in U.S.patent application Ser. No. 11/534,166 entitled “Methods and Systems forImage Data Processing” filed Sep. 21, 2006 by Roth, which isincorporated by reference herein.

The processor may be a processor such as those commonly included in atypical personal computer, mainframe computer system, workstation, etc.In general, the term “computer system” may be broadly defined toencompass any device having one or more processors, which executesinstructions from a memory medium. The processor may be implementedusing any other appropriate functional hardware. For example, theprocessor may include a digital signal processor (DSP) with a fixedprogram in firmware, a field programmable gate array (FPGA), or otherprogrammable logic device (PLD) employing sequential logic “written” ina high level programming language such as very high speed integratedcircuits (VHSIC) hardware description language (VHDL). In anotherexample, program instructions (not shown) executable on the processor toperform one or more steps of the computer-implemented methods describedin the above-referenced patent application may be coded in a high levellanguage such as C#, with sections in C++ as appropriate, ActiveXcontrols, JavaBeans, Microsoft Foundation Classes (“MFC”), or othertechnologies or methodologies, as desired. The program instructions maybe implemented in any of various ways, including procedure-basedtechniques, component-based techniques, and/or object-orientedtechniques, among others. Program instructions may be transmitted overor stored on a carrier medium (not shown). The carrier medium may be atransmission medium such as a wire, cable, or wireless transmissionlink. The carrier medium may also be a storage medium such as aread-only memory, a random access memory, a magnetic or optical disk, ora magnetic tape.

The embodiments of an imaging system of FIGS. 1-4 are configured tosubstantially immobilize one or more particles 40 in an imaging chamber42 of the measurement device. Preferably, this system includes magneticelement 264 positioned on the side of imaging chamber 42 opposite theoptics of the system. Magnetic element 264 may include any suitablemagnetic element known in the art such as a permanent magnet or anelectromagnet that can be used to generate a suitable magnetic field. Inthis manner, dyed particles with embedded magnetite may be used in theembodiments described herein such that the particles can besubstantially immobilized in imaging chamber 42 (e.g., at the bottom ofthe chamber) using a magnetic field generated by magnetic element 264 atthe back side of the chamber 42. Although magnetic element 264 is shownspaced from imaging chamber 42 in several figures, the magnetic element264 may also be in contact with (or coupled to) imaging chamber 42 onthe side of the imaging chamber opposite the optical elements of thesystem. Magnetic element 264 may be further configured as describedabove. FIG. 3 shows a side view of an imaging chamber with magnet 264positioned proximate to a surface of the chamber such that beads 40 aresubstantially immobilized on the surface of the chamber. FIG. 3illustrates an embodiment in which the fluorophores are attached to thesurface of the beads. FIG. 4 also shows a side view of an imagingchamber with magnet 264 positioned proximate to a surface of the chambersuch that beads 40 are substantially immobilized on the surface of thechamber. In FIG. 4, however, the fluorophores are attached to nucleicacid sequences (e.g., PCR primers) that are not directly coupled tobeads 40, but rather associate with beads 40 via hybridization tosequences that are directly coupled to the beads. This results in “freefloating” fluorophores when a complementary probe sequence on a bead isnot available for hybridization with the nucleic acid sequence to whichthe fluorophore is attached. Signals from these free floatingfluorophores can increase the background noise when imaging the beadsimmobilized on the surface of the chamber; however, since the freefloating fluorophores are generally not in the focal plane of imagingsystem, successful imaging of the beads can be achieved. the Inaddition, although various FIGs show one magnetic element positionedproximate the imaging chamber, it is to be understood that the systemmay include more than one magnetic element, each of which is positionedproximate the side of the imaging chamber opposite the optics of thesystem.

The system may include a magnet that is affixed such that magnet iscapable of moving to various distances with respect to the imagingchamber 42. After signal acquisition by the imaging system, the magneticfield may be removed (e.g., by using a solenoid to move a permanentmagnet or by turning an electromagnet on and off with a switch), and theparticles 40 may exit the imaging chamber, while new particles 40 fromthe next sample are brought into the chamber. The particles in theimaging chamber 42 may be removed and particles may be introduced to theimaging chamber using any of the embodiments described herein. Inanother embodiment, the particles in the imaging chamber 42 may bereleased from the surface and remain in the chamber, to interact withother elements in solution and then pulled to the surface again forimaging.

In one embodiment, the imaging chamber design is an imaging chamber thathas a relatively smooth internal surface on the side of the imagingchamber proximate the magnetic element 264 such that the beads 40 arerandomly distributed across this internal surface as the magnet 264pulls them to the surface. However, the imaging chamber 42 can also bedesigned to “hold” the beads in particular spots when the magnetic fieldis applied. For example, the internal surface of the imaging chambershown in FIG. 1 may have a square pattern of etched recesses formedtherein such that a bead 40 is disposed in one of the etched recessesupon application of a magnetic field as described above. Such etchedrecesses assist in separating the beads as the magnetic field isapplied. The “etched” recesses may be formed by an etching process orany other suitable process known in the art. Furthermore, theconfiguration and arrangement of the etched recesses may vary dependingon, for example, the size of the beads 40 and the selected spacingbetween the beads.

In another example, an internal surface of an imaging chamber 42 mayhave a triangle pattern of etched recesses such that bead 40 is disposedin one of the etched recesses upon application of a magnetic field asdescribed above. Therefore, etched recesses assist in separating thebeads as the magnetic field is applied. In addition, the “etched”recesses may be formed by an etching process or any other suitableprocess known in the art. Furthermore, the configuration and arrangementof the etched recesses may vary depending on, for example, the size ofthe beads and the selected spacing between the beads. Although etchedrecesses are preferably two-dimensional in the sense that the beads 40are confined by the recesses in two dimensions, these recesses can bereplaced by trenches or any other suitable recesses that are configuredto confine the beads in only one direction.

Other embodiments exist relating to methods for substantiallyimmobilizing one or more particles 40 in an imaging volume of ameasurement device. Substantially immobilizing the one or more particlesmay be performed as described herein using magnetic attraction, a vacuumfilter substrate or in other ways known in the art. For example,substantially immobilizing the one or more particles in an imagingvolume of a measurement device may include applying a magnetic field toone side of an imaging chamber that defines the imaging volume of themeasurement device. In addition, this method may include any otherstep(s) described herein.

Furthermore, this method may be performed by any of the systemsdescribed herein. Examples of methods and systems for positioningmicrospheres for imaging are illustrated in U.S. patent application Ser.No. 11/270,786 to Pempsell filed Nov. 9, 2005, which is incorporated byreference herein. Regardless of the particle immobilization method, theparticles are preferably substantially immobilized such that theparticles do not move perceptibly during the detector integrationperiod, which may be multiple seconds long.

A further embodiment relates to a system configured to transfer one ormore particles to an imaging volume of a measurement device from one ormore storage vessels (e.g., an aliquot introduced to the system of FIG.10), to image the one or more particles in the imaging volume, tosubstantially immobilize the one or more materials in the imagingvolume, or some combination thereof. The system may be configured totransfer the one or more particles as described herein, to image the oneor more particles as described herein, to substantially immobilize theone or more particles as described herein, or some combination thereof.

The measurements described herein generally include image processing foranalyzing one or more images of particles to determine one or morecharacteristics of the particles such as numerical values representingthe magnitude of fluorescence emission of the particles at multipledetection wavelengths. Subsequent processing of the one or morecharacteristics of the particles such as using one or more of thenumerical values to determine a token ID representing the multiplexsubset to which the particles belong and/or a reporter valuerepresenting a presence and/or a quantity of analyte bound to thesurface of the particles can be performed according to the methodsdescribed in U.S. Pat. No. 5,736,330 to Fulton, U.S. Pat. No. 5,981,180to Chandler et al., U.S. Pat. No. 6,449,562 to Chandler et al., U.S.Pat. No. 6,524,793 to Chandler et al., U.S. Pat. No. 6,592,822 toChandler, and U.S. Pat. No. 6,939,720 to Chandler et al, which areincorporated by reference herein.

In one example, techniques described in U.S. Pat. No. 5,981,180 toChandler et al. may be used with the fluorescent measurements describedherein in a multiplexing scheme in which the particles are classifiedinto subsets for analysis of multiple analytes in a single sample.Additional examples of systems that may be configured as describedherein (e.g., by inclusion of an embodiment of an illumination subsystemdescribed herein) are illustrated in U.S. Pat. No. 5,981,180 to Chandleret al., U.S. Pat. No. 6,046,807 to Chandler, U.S. Pat. No. 6,139,800 toChandler, U.S. Pat. No. 6,366,354 to Chandler, U.S. Pat. No. 6,411,904to Chandler, U.S. Pat. No. 6,449,562 to Chandler et al, and U.S. Pat.No. 6,524,793 to Chandler et al, which are incorporated by referenceherein. The system shown in FIG. 10 may also be further configured asdescribed in these patents. The system shown in FIG. 10 may be furtherconfigured as described herein with respect to other systems andembodiments.

Another embodiment of the imaging systems of FIGS. 1 and 2 configured toperform measurements of particles is shown in FIG. 9. The system shownin FIG. 9 may be used in applications such as multi-analyte measurementof a sample. This embodiment of the system is configured as afluorescence imaging system. The system includes an illuminationsubsystem configured to provide illumination of the particles 62 duringmeasurement. In FIG. 9 the illumination subsystem includes LED or LEDdie 108. LED or LED die 108 may include any appropriate LED or LED dieknown in the art. In addition, the illumination subsystem may includemore than one light source (not shown), each of which is configured togenerate light of at least one wavelength or at least one wavelengthband. One example of an appropriate combination of light sources for usein the system shown in FIG. 9 includes, but is not limited to, two ormore LEDs or LED dies. It is to be understood that a single LED die maycontain either a single emission area (of any shape) or multipleemission areas on a single die. Typically, if these multiple emissionareas are rectangularly shaped they are referred to as “bars.” The lightsources, however, may include at least one LED die in combination withone or more other non-LED light sources such as those described above.Light generated by more than one light source may be combined into acommon illumination path by a beamsplitter (not shown) or any othersuitable optical element known in the art such that light from the lightsources may be directed to the particles simultaneously.

Alternatively, the illumination subsystem may include an optical element(not shown) such as a reflecting mirror and a device (not shown)configured to move the optical element into and out of the illuminationpath depending on which light source is used to illuminate theparticles. In this manner, the light sources may be used to sequentiallyilluminate the particles with different wavelengths or wavelength bandsof light. The light source(s) may also illuminate the substrate fromabove (not shown), rather than from below the substrate.

The light source(s) may be selected to provide light at wavelength(s) orwavelength band(s) that will cause the particles or materials coupledthereto or incorporated therein to emit fluorescence. For instance, thewavelength(s) or wavelength band(s) may be selected to excitefluorophores, fluorescent dyes, or other fluorescent materialsincorporated into the particles and/or coupled to a surface of theparticles. In this manner, the wavelength(s) or wavelength band(s) maybe selected such that the particles emit fluorescence that is used forclassification of the particles. In addition, the wavelength(s) orwavelength band(s) may be selected to excite fluorophores, fluorescentdyes, quantum dots, fluorescent nanocrystals, or other fluorescentmaterials coupled to the particles via a reagent on the surface of theparticles or internal to the particles. As such, the wavelength(s) orwavelength band(s) may be selected such that the particles emitfluorescence that is used to detect and/or quantify reaction(s) thathave taken place on the surface of the particles or internal to theparticles. Alternatively, the wavelength(s) or wavelength band(s) may beselected to excite the particles themselves such that the particles emitfluorescence that can be used to determine physical size characteristicsof the particles and/or the existence of a type of particle such thatsubsequent testing may be selected. An example of an application forsuch a system is a biodefense application in which output responsive tothe fluorescence and/or scattering of particles can be used to detect ata minimum, the potential presence of biological or chemical pathogens.

In addition to detection, a certain set of physical and/or opticalcharacteristics may be analyzed using the output. The illuminationsubsystem also includes reflector 110 that is substantially ellipticaland is disposed in an optical path of the light generated by LED or LEDdie 108. Reflector 110 is configured to direct light from the LED or LEDdie to an illumination volume such that an intensity of the lightthroughout the illumination volume is substantially uniform. LED or LEDdie 108 and reflector 110 may be further configured as described herein.Particles 40 are disposed in the illumination volume during measurement.In particular, reflector 110 is configured to direct light from LED orLED die 108 to substrate 114 on which particles 40 are immobilized.Particles 40 may include any of the particles described above. Substrate114 may include any appropriate substrate known in the art. Theparticles immobilized on substrate 114 may be disposed in an imagingchamber (not shown) or any other device for maintaining a position ofsubstrate 114 and particles 40 immobilized thereon with respect to theillumination subsystem. The device for maintaining a position ofsubstrate 114 may also be configured to alter a position of thesubstrate (e.g., to focus the illumination onto the substrate) prior toimaging.

Immobilization of the particles 40 on the substrate 114 of FIG. 9 may beperformed using magnetic attraction as discussed above, a vacuum filterplate, or any other appropriate method known in the art as discussedabove. However, the particles 40 are preferably immobilized such thatthe particles do no move perceptibly during the detector integrationperiod, which may be multiple seconds long.

The system shown in FIG. 9 also includes a detection subsystem that isconfigured to generate output responsive to light from (e.g., scatteredfrom and/or emitted by) the particles in the imaging volume. Forexample, as shown in FIG. 9, the detection subsystem may include opticalelement 116 and dichroic beamsplitter 118. Optical element 116 isconfigured to collect and collimate light from substrate 114 andparticles 40 immobilized thereon and to direct the light to beamsplitter118. Optical element 116 may include any appropriate optical elementknown in the art. In addition, although optical element 116 is shown inFIG. 9 as a single optical element, it is to be understood that opticalelement 116 may include more than one optical element. Furthermore,although optical element 116 is shown in FIG. 9 as a refractive opticalelement, it is to be understood that optical element 116 may include oneor more reflective optical elements, one or more refractive opticalelements, one or more diffractive optical elements, or some combinationthereof.

Beamsplitter 118 may include any appropriate beamsplitter known in theart. Beamsplitter 118 may be configured to direct light from opticalelement 116 to different detectors based on the wavelength of the light.For example, light having a first wavelength or wavelength band may betransmitted by beamsplitter 118, and light having a second wavelength orwavelength band different than the first may be reflected bybeamsplitter 118. The detection subsystem may also include opticalelement 120 and detector 122. Light transmitted by beamsplitter 118 maybe directed to optical element 120. Optical element 120 is configured tofocus the light transmitted by the beamsplitter onto detector 122. Thedetection subsystem may further include optical element 124 and detector126. Light reflected by beamsplitter 118 may be directed to opticalelement 124. Optical element 124 is configured to focus the lightreflected by the beamsplitter onto detector 126. Optical elements 120and 124 may be configured as described above with respect to opticalelement 116.

Detectors 122 and 126 may include, for example, charge coupled device(CCD) detectors or any other suitable imaging detectors known in the artsuch as CMOS detectors, two-dimensional arrays of photosensitiveelements, time delay integration (TDI) detectors, etc. In someembodiments, a detector such as a two-dimensional CCD imaging array maybe used to acquire an image of substantially an entire substrate or ofall particles immobilized on a substrate simultaneously. The number ofdetectors included in the system may be equal to the number ofwavelengths or wavelength bands of interest such that each detector isused to generate images at one of the wavelengths or wavelength bands.Each of the images generated by the detectors may be spectrally filteredusing an optical bandpass element (not shown) or any other suitableoptical element known in the art, which is disposed in the light pathfrom the beamsplitter to the detectors. A different filter “band” may beused for each captured image. The detection wavelength center and widthfor each wavelength or wavelength band at which an image is acquired maybe matched to the fluorescent emission of interest, whether it is usedfor particle classification or the reporter signal. In this manner, thedetection subsystem of the system shown in FIG. 9 is configured togenerate multiple images at different wavelengths or wavelength bandssimultaneously.

Although the system shown in FIG. 9 includes two detectors, it is to beunderstood that the system may include more than two detectors (e.g.,three detectors, four detectors, etc.). As described above, thedetectors may be configured to generate images at different wavelengthsor wavelength bands simultaneously by using one or more optical elementsfor directing light at different wavelengths or wavelength bands to thedifferent detectors simultaneously. In addition, although the system isshown in FIG. 9 to include multiple detectors, it is to be understoodthat the system may include a single detector. The single detector maybe used to generate multiple images at multiple wavelengths orwavelength bands sequentially. For example, light of differentwavelengths or wavelength bands may be directed to the substratesequentially, and different images may be generated during illuminationof the substrate with each of the different wavelengths or wavelengthbands.

In another example, different filters for selecting the wavelength orwavelength band of light directed to the single detector may be altered(e.g., by moving the different filters into and out of the imaging path)to generate images at different wavelengths or wavelength bandssequentially. The detection subsystem shown in FIG. 9, therefore, isconfigured to generate a plurality or series of images representing thefluorescent emission of particles 112 at several wavelengths ofinterest. In addition, the system may be configured to supply aplurality or series of digital images representing the fluorescenceemission of the particles to a processor (i.e., a processing engine). Inone such example, the system may include processor 128. Processor 128may be configured to acquire (e.g., receive) image data from detectors122 and 126. For example, processor 128 may be coupled to detectors 122and 126 in any suitable manner known in the art (e.g., via transmissionmedia (not shown), each coupling one of the detectors to the processor,via one or more electronic components (not shown) such asanalog-to-digital converters, each coupled between one of the detectorsand the processor, etc.). Preferably, processor 128 is configured toprocess and analyze the images to determine one or more characteristicsof particles 40 such as a classification of the particles andinformation about an analyte on the surface of the particles. The one ormore characteristics may be output by the processor in any suitableformat such as a data array with an entry for fluorescent magnitude foreach particle for each wavelength or wavelength band. Processor 128 maybe a processor such as those commonly included in a typical personalcomputer, mainframe computer system, workstation, etc. In general, theterm “computer system” may be broadly defined to encompass any devicehaving one or more processors, which executes instructions from a memorymedium. The processor may be implemented using any other appropriatefunctional hardware. For example, the processor may include a DSP with afixed program in firmware, a field programmable gate array (FPGA), orother programmable logic device (PLD) employing sequential logic“written” in a high level programming language such as very high speedintegrated circuits (VHSIC) hardware description language (VHDL).

In another example, program instructions (not shown) executable onprocessor 128 may be coded in a high level language such as C#, withsections in C++ as appropriate, ActiveX controls, JavaBeans, MicrosoftFoundation Classes (“MFC”), or other technologies or methodologies, asdesired. The program instructions may be implemented in any of variousways, including procedure-based techniques, component-based techniques,and/or object-oriented techniques, among others.

The system shown in FIG. 9 may be further configured as described hereinwith respect to other systems and embodiments.

FIG. 10 illustrates a flow cytometer embodiment of an imaging systemconfigured to perform measurements of particles in accordance withcertain embodiments of the present invention. The system illustrated inFIG. 10 includes an illumination subsystem configured according to theembodiments described herein. In FIG. 10, the system is shown along aplane through the cross section of cuvette 72 through which particles 74flow. In one example, the cuvette may be a standard fused silica cuvettesuch as that used in standard flow cytometers. However, any othersuitable type of viewing or delivery configuration, such as a suitablyconfined sample air-flow stream may also be used to deliver the samplefor analysis. Applying the method of real-time PCR to the system of FIG.10 entails transferring an aliquot of the PCR solution from the thermalcycler to the detection system of FIG. 10. By taking an aliquot atdifferent intervals of the PCR process, quantitation of the initialtemplate or DNA is facilitated. This method may also manipulate thealiquots by adding additional buffers or reagents, or amplificationmethods that may improve detection. Other methods may includepre-aliquoting PCR reagents prior to loading in a thermal cycler, andremoving these samples at separate intervals in the PCR process, or anyother assay process.

The illumination subsystem is configured to illuminate particles 74 withlight. The illumination subsystem includes LED or LED die 76. The LED orLED die may be any suitable LED or LED die known in the art. Inaddition, the illumination subsystem may include more than one LED orLED die (not shown). In other embodiments, the illumination subsystemincludes LED or LED die 76 and one or more other light sources (notshown) such as LEDs, LED dies, lasers, arc lamps, fiber illuminators,light bulbs, or some combination thereof. The other light source(s) mayinclude any suitable such light source(s) known in the art. In thismanner, the illumination subsystem may include more than one lightsource. In one embodiment, the light sources may be configured toilluminate the particles with light having different wavelengths orwavelength bands (e.g., blue light and green light). In someembodiments, the light sources may be configured to illuminate theparticles at different directions.

The illumination subsystem also includes reflector 78 that issubstantially elliptical and is configured to direct light from LED orLED die 76 to an illumination volume such that an intensity of the lightthroughout the illumination volume is substantially uniform or has aselected illumination function in the illumination volume. LED or LEDdie 76 and reflector 78 may be further configured as described herein.Particles 74 flow through the illumination volume during measurement. Inthis manner, light exiting reflector 78 illuminates the particles asthey flow through the cuvette. The illumination may cause the particlesthemselves or a fluorophore attached thereto or incorporated therein toemit fluorescent light having one or more wavelengths or wavelengthbands. The fluorophore may include any appropriate fluorophore known inthe art. In some embodiments, particles 74 themselves are configured toemit fluorescence or to naturally emit fluorescence when illuminatedwith light of appropriate intensity and wavelength. In one suchembodiment, the light exiting reflector 78 causes the particles to emitfluorescence.

The system shown in FIG. 10 also includes a detection subsystemconfigured to generate output responsive to light from (e.g., scatteredfrom and/or emitted by) particles in the illumination volume. Forexample, light scattered forwardly from the particles may be directed todetection system 80 by optical element 82, which may be a foldingmirror, a suitable light directing component, or a dichroic reflectingcomponent. Alternatively, detection system 80 may be placed directly inthe path of the forwardly scattered light. In this manner, opticalelement 82 may not be included in the system. In one embodiment, theforwardly scattered light may be light scattered by the particles at anangle of about 180° from the direction of illumination by theillumination subsystem, as shown in FIG. 10. The angle of the forwardlyscattered light may not be exactly 180° from the direction ofillumination such that incident light may not impinge upon thephotosensitive surface of the detection system. For example, theforwardly scattered light may be light scattered by the particles atangles less than or greater than 180° from the direction of illumination(e.g., light scattered at an angle of about 170°, about 175°, about185°, or about 190°). Light scattered by the particles at an angle ofabout 90° from the direction of illumination may also be collected bythe detection subsystem. Light scattered by the particles can also oralternatively be collected at any angle or orientation by the detectionsubsystem.

In one embodiment, this scattered light may be separated into more thanone beam of light by one or more beamsplitters or dichroic mirrors. Forexample, light scattered at an angle of about 90° to the direction ofillumination may be separated into two different beams of light bybeamsplitter 84. The two different beams of light may be separated againby beamsplitters 86 and 88 to produce four different beams of light.Each of the beams of light may be directed to a different detectionsystem, which may include one or more detectors. For example, one of thefour beams of light may be directed to detection system 90. Detectionsystem 90 may be configured to detect light scattered by the particles.Scattered light detected by detection system 80 and/or detection system90 may generally be proportional to the volume of the particles that areilluminated by the light source. Therefore, output of detection system80 and/or output of detection system 90 may be used to determine adiameter of the particles that are in the illumination volume.

In addition, the output of detection system 80 and/or detection system90 may be used to identify more than one particle that are stucktogether or that are passing through the illumination volume atapproximately the same time. Therefore, such particles may bedistinguished from other sample particles and calibration particles. Theother three beams of light may be directed to detection systems 92, 94,and 96. Detection systems 92, 94, and 96 may be configured to detectfluorescence emitted by the fluorophore or the particles themselves.Each of the detection systems may be configured to detect fluorescenceof a different wavelength or a different range of wavelengths. Forexample, one of the detection systems may be configured to detect greenfluorescence. Another of the detection systems may be configured todetect yellow-orange fluorescence, and the other detection system may beconfigured to detect red fluorescence.

In some embodiments, spectral filters 98, 100, and 102 may be coupled todetection systems 92, 94, and 96, respectively. The spectral filters maybe configured to block fluorescence of wavelengths other than that orthose which the detection systems are configured to detect. In addition,one or more lenses (not shown) may be optically coupled to each of thedetection systems. The lenses may be configured to focus the scatteredlight or emitted fluorescence onto a photosensitive surface of thedetectors. The detector's output is proportional to the fluorescentlight impinging on it and results in a current pulse. The current pulsemay be converted to a voltage pulse, low pass filtered, and thendigitized by an A/D converter (not shown). Processor 104 such as adigital signal processor (DSP) integrates the area under the pulse toprovide a number that represents the magnitude of the fluorescence. Asshown in FIG. 10, processor 104 may be coupled to detector 90 viatransmission medium 106. Processor 104 may also be coupled to detector90 indirectly via transmission medium 106 and one or more othercomponents (not shown) such as the A/D converter. The processor may becoupled to other detectors of the system in a similar manner. Processor104 may be further configured as described herein.

In some embodiments, the output responsive to fluorescence emitted bythe fluorophore or particles may be used to determine an identity of theparticles and information about a reaction taken or taking place on thesurface of the particles. For example, output of two of the detectionsystems may be used to determine an identity of the particles, andoutput of the other detection system may be used to determine a reactiontaken or taking place on the surface of the particles. Therefore, theselection of the detectors and the spectral filters may vary dependingon the type of dyes or fluorophores incorporated into or bound to theparticles and/or the reaction being measured (i.e., the dye(s)incorporated into or bound to the reactants involved in the reaction),or may depend upon the fluorescence characteristics of the particlesthemselves. The detection systems that are used to determine an identityof the sample particles (e.g., detection systems 92 and 94) may beavalanche photodiodes (APDs), photomultiplier tubes (PMTs), or anothertype of photodetector. The detection system that is used to identify areaction taken or taking place on the surface of the particles (e.g.,detection system 96) may be a PMT, an APD, or another type ofphotodetector. The measurement system may be further configured asdescribed herein.

Although the system of FIG. 10 includes two detection systems fordistinguishing between particles having different dye characteristics,it is to be understood that the system may include more than twodetection systems (i.e., 3 detection systems, 4 detection systems, etc.)for distinguishing between particles having different dyecharacteristics. In such embodiments, the system may include additionalbeamsplitters and additional detection systems. In addition, spectralfilters and/or lenses may be coupled to each of the additional detectionsystems.

In certain embodiments, the systems disclosed herein include a thermalcontrol element coupled to the imaging chamber 42. With the thermalcontrol element coupled to the imaging chamber 42 the temperature in theimaging chamber may be adjusted as needed for performing variousbiological reactions. Accordingly, by coupling a thermal control elementcoupled to the imaging chamber PCR may be performed within the imagingchamber 42. In certain aspects, the imaging chamber may be coupled to adevice for release of microspheres from the surface of the chamber,including sonication or vortexing devices. Other embodiments includesystems having multiple detection chambers and/or disposable detectionchambers.

B. PCR

The polymerase chain reaction (PCR) is a technique widely used inmolecular biology to amplify a piece of DNA by in vitro enzymaticreplication. Typically, PCR applications employ a heat-stable DNApolymerase, such as Taq polymerase. This DNA polymerase enzymaticallyassembles a new DNA strand from nucleotides (dNTPs) usingsingle-stranded DNA as template and DNA primers to initiate DNAsynthesis. A basic PCR reaction requires several components and reagentsincluding: a DNA template that contains the target sequence to beamplified; one or more primers, which are complementary to the DNAregions at the 5′ and 3′ ends of the target sequence; a DNA polymerase(e.g., Taq polymerase) that preferably has a temperature optimum ataround 70° C.; deoxynucleotide triphosphates (dNTPs); a buffer solutionproviding a suitable chemical environment for optimum activity andstability of the DNA polymerase; divalent cations, typically magnesiumions (Mg2⁺); and monovalent cation potassium ions.

The majority of PCR methods use thermal cycling to subject the PCRsample to a defined series of temperature steps. Each cycle typicallyhas 2 or 3 discrete temperature steps. The cycling is often preceded bya single temperature step (“initiation”) at a high temperature (>90°C.), and followed by one or two temperature steps at the end for finalproduct extension (“final extension”) or brief storage (“final hold”).The temperatures used and the length of time they are applied in eachcycle depend on a variety of parameters. These include the enzyme usedfor DNA synthesis, the concentration of divalent ions and dNTPs in thereaction, and the melting temperature (Tm) of the primers. Commonly usedtemperatures for the various steps in PCR methods are: initializationstep —94-96° C.; denaturation step —94-98° C.; annealing step —50-65°C.; extension/elongation step —70-74° C.; final elongation —70-74° C.;final hold —4-10° C.

Real-time polymerase chain reaction, also called quantitative real timepolymerase chain reaction (QRT-PCR) or kinetic polymerase chainreaction, is used to amplify and simultaneously quantify a targeted DNAmolecule. It enables both detection and quantification (as absolutenumber of copies or relative amount when normalized to DNA input oradditional normalizing genes) of a specific sequence in a DNA sample.Real-time PCR may be combined with reverse transcription polymerasechain reaction to quantify low abundance RNAs. Relative concentrationsof DNA present during the exponential phase of real-time PCR aredetermined by plotting fluorescence against cycle number on alogarithmic scale. Amounts of DNA may then be determined by comparingthe results to a standard curve produced by real-time PCR of serialdilutions of a known amount of DNA.

Multiplex-PCR and multiplex real-time PCR use of multiple, unique primersets within a single PCR reaction to produce amplicons of different DNAsequences. By targeting multiple genes at once, additional informationmay be gained from a single test run that otherwise would requireseveral times the reagents and more time to perform. Annealingtemperatures for each of the primer sets should be optimized to workwithin a single reaction.

The methods disclosed herein may also utilize asymmetric primingtechniques during the PCR process, which may enhance the binding of thereporter probes to complimentary target sequences. Asymmetric PCR iscarried with an excess of the primer for the chosen strand topreferentially amplify one strand of the DNA template more than theother.

C. Real-Time PCR Detection Chemistries

There are several commercially available nucleic acid detectionchemistries currently used in real-time PCR. These chemistries includeDNA binding agents, FRET based nucleic acid detection, hybridizationprobes, molecular beacons, hydrolysis probes, and dye-primer basedsystems. Each of these chemistries is discussed in more detail below.

1. DNA Binding Agents

The first analysis of kinetic PCR was performed by Higuchi et al. whoused ethidium bromide to bind double-stranded DNA products (Higuchi etal., 1992; Higuchi et al., 1993; U.S. Pat. No. 5,994,056; U.S. PublishedApplication No. 2001/6171785). Ethidium bromide, like all other DNAbinding agents used in kinetic PCR, is able to increase in fluorescentintensity upon binding. The resulting increase in signal can be recordedover the course of the reaction, and plotted versus the cycle number.Recording the data in this way is more indicative of the initialconcentration of the sample of interest compared to end-point analysis.

Binding dyes are relatively inexpensive as compared to other detectionchemistries. The advantages of using these binding dyes are their lowcost and excellent signal to noise ratios. Disadvantages include theirnon-specific binding properties to any double-stranded DNA in the PCRreaction, including amplicons created by primer-dimer formations(Wittwer et al., 1997). In order to confirm the production of a specificamplicon, a melting curve analysis should be performed (Ishiguro et al.,1995). Another drawback is that amplification of a longer product willgenerate more signal than a shorter one. If amplification efficienciesare different, quantification may be even more inaccurate (Bustin andNolan, 2004).

SYBR® Green I from Invitrogen™ (Carlsbad, Calif.) is a popularintercalating dye (Bengtsson et al., 2003). SYBR® Green I is acyclically substituted asymmetric cyanine dye (Zipper et al, 2004; U.S.Pat. Nos. 5,436,134; 5,658,751). A minor groove binding asymmetriccyanine dye known as BEBO, has been used in real-time PCR. BEBO causes anon-specific increase in fluorescence with time, perhaps due to a slowaggregation process and is less sensitive compared to SYBR® Green I. Asimilar dye called BOXTO has also been reported for use in qPCR(Bengtsson et al., 2003; U.S. Published Application No. 2006/0211028).Like BEBO, BOXTO is less sensitive than SYBR® Green I (U.S. PublishedApplication No. 2006/0211028).

Other common reporters include YO-PRO-1 and thiazole orange (TO) whichare intercalating asymmetric cyanine dyes (Nygren et al., 1998). Whilethese dyes exhibit large increases in fluorescence intensity uponbinding, TO and Oxazole Yellow (YO) have been reported to perform poorlyin real-time PCR (Bengtsson et al., 2003). Other dyes that may be usedinclude, but are not limited to, pico green, acridinium orange, andchromomycin A3 (U.S. Published Application No. 2003/6569627). Dyes thatmay be compatible with real-time PCR can be obtained from variousvendors such as, Invitrogen, Cambrex Bio Science (Walkersville, Md.),Rockland Inc. (Rockland, Me.), Aldrich Chemical Co. (Milwaukee, Wis.),Biotium (Hayward, Calif.), TATAA Biocenter AB. (Goteborg, Sweden) andIdaho Technology (Salt Lake City, Utah) (U.S. Published Application No.2007/0020672).

A dye known as EvaGreen™ (Biotium) has shown promise in that it isdesigned to not inhibit PCR, and is more stable in alkaline conditionsas compared to SYBR® Green I (Dorak, 2006; U.S. Published ApplicationNo. 2006/0211028). Other newer dyes include the LCGreen® dye family(Idaho Technology). LCGreen® I and LCGreen® Plus are the mostcommercially competitive of these dyes. LCGreen® Plus is considerablybrighter than LCGreen® (U.S. Published Application No. 2007/0020672;Dorak, 2006; U.S. Published Application No. 2005/0233335; U.S. PublishedApplication No. 2066/0019253).

2. FRET Based Nucleic Acid Detection

Many real-time nucleic acid detection methods utilize labels thatinteract by Forster Resonance Energy Transfer (FRET). This mechanisminvolves a donor and acceptor pair wherein the donor molecule is excitedat a particular wavelength, and subsequently transfers its energynon-radiatively to the acceptor molecule. This typically results in asignal change that is indicative of the proximity of the donor andacceptor molecules to one another.

Early methods of FRET based nucleic acid detection that lay a foundationfor this technology in general, include work by Heller et al. (U.S. Pat.Nos. 4,996,143; 5,532,129; and 5,565,322, which are incorporated byreference). These patents introduce FRET based nucleic acid detection byincluding two labeled probes that hybridize to the target sequence inclose proximity to each other. This hybridization event causes atransfer of energy to produce a measurable change in spectral response,which indirectly signals the presence of the target.

Cardullo et al. (incorporated by reference) established thatfluorescence modulation and nonradiative fluorescence resonance energytransfer can detect nucleic acid hybridization in solution (Cardullo etal., 1988). This study used three FRET based nucleic acid detectionstrategies. The first includes two 5′ labeled probes that werecomplementary to one another, allowing transfer to occur between a donorand acceptor fluorophore over the length of the hybridized complex. Inthe second method, fluorescent molecules were covalently attached to twonucleic acids, one at the 3′ end and the other at the 5′ end. Thefluorophore-labeled nucleic acids hybridized to distinct but closelyspaced sequences of a longer, unlabeled nucleic acid. Finally, anintercalating dye was used as a donor for an acceptor fluorophore thatwas covalently attached at the 5′ end of the probe.

Morrison et al. (1989), incorporated by reference, used complementarylabeled probes to detect unlabeled target DNA by competitivehybridization, producing fluorescence signals which increased withincreasing target DNA concentration. In this instance, two probes wereused that were complementary to one another and labeled at their 5′ and3′ ends with fluorescein and fluorescein quencher, respectively. Laterwork also showed that fluorescence melting curves could be used tomonitor hybridization (Morrison and Stols, 1993).

3. Hybridization Probes

Hybridization probes used in real-time PCR were developed mainly for usewith the Roche LightCycler® instruments (U.S. Published Application No.2001/6174670; U.S. Published Application No. 2000/6140054). These aresometimes referred to as FRET probes, LightCycler® probes, or dual FRETprobes (Espy et al., 2006).

Hybridization probes are used in a format in which FRET is measureddirectly (Wilhelm and Pingoud, 2003). Each of the two probes is labeledwith a respective member of a fluorescent energy transfer pair, suchthat upon hybridization to adjacent regions of the target DNA sequence,the excitation energy is transferred from the donor to the acceptor, andsubsequent emission by the acceptor can be recorded as reporter signal(Wittwer et al., 1997). The two probes anneal to the target sequence sothat the upstream probe is fluorescently labeled at its 3′ end and thedownstream probe is labeled at its 5′ end. The 3′ end of the downstreamprobe is typically blocked by phosphorylation or some other means toprevent extension of the probe during PCR. The dye coupled to the 3′ endof the upstream probe is sufficient to prevent extension of this probe.This reporter system is different from other FRET based detectionmethods (molecular beacons, TaqMan®, etc.) in that it uses FRET togenerate rather than to quench the fluorescent signal (Dorak, 2006).

Typical acceptor fluorophores include the cyanine dyes (Cy3 and Cy5),6-carboxy-4,7,2′,7′-tetrachlorofluorescein (TET),6-carboxy-N,N,N′,N′-tetramethylrhodamine (TAMRA), and 6-carboxyrhodamineX (ROX). Donor fluorophores are usually 6-carboxyfluoroscein (FAM)(Wilhelm and Pingoud, 2003). Hybridization probes are particularlyadvantageous for genotyping and mismatch detection. Melting curveanalysis can be performed in addition to the per-cycle monitoring offluorescence during the PCR reaction. A slow heating of the sample afterprobe hybridization can provide additional qualitative information aboutthe sequence of interest (Lay and Wittwer, 1997; Bernard et al., 1998a;Bernard et al., 1998b). Base-pair mismatches will shift the stability ofa duplex, in varying amounts, depending on the mismatch type andlocation in the sequence (Guo et al., 1997).

4. Molecular Beacons

Molecular beacons, also known as hairpin probes, are stem-loopstructures that open and hybridize in the presence of a complementarytarget sequence, typically causing an increase in fluorescence (U.S.Pat. No. 5,925,517); U.S. Published Application No. 2006/103476).Molecular beacons typically have a nucleic acid target complementsequence flanked by members of an affinity pair that, under assayconditions in the absence of target, interact with one another to form astem duplex. Hybridization of the probes to their preselected targetsequences produces a conformational change in the probes, forcing the“arms” apart and eliminating the stem duplex and thereby separating thefluorophore and quencher.

5. Hydrolysis Probes

Hydrolysis probes, also known as the TaqMan® assay (U.S. Pat. No.5,210,015), are popular because they only involve a single probe pertarget sequence, as opposed to two probes (as in hybridization probes).This results in a cost savings per sample. The design of these probes isalso less complicated than that of molecular beacons. These aretypically labeled with a reporter on the 5′ end and a quencher on the 3′end. When the reporter and quencher are fixed onto the same probe, theyare forced to remain in close proximity. This proximity effectivelyquenches the reporter signal, even when the probe is hybridized to thetarget sequence. During the extension or elongation phase of the PCRreaction, a polymerase known as Taq polymerase is used because of its 5′exonuclease activity. The polymerase uses the upstream primer as abinding site and then extends. Hydrolysis probes are cleaved duringpolymerase extension at their 5′ end by the 5′-exonuclease activity ofTaq. When this occurs, the reporter fluorophore is released from theprobe, and subsequently, is no longer in close proximity to thequencher. This produces a perpetual increase in reporter signal witheach extension phase as the PCR reaction continues cycling. In order toensure maximal signal with each cycle, hydrolysis probes are designedwith a Tm that is roughly 10° C. higher than the primers in thereaction.

However, the process of cleaving the 5′ end of the probe need notrequire amplification or extension of the target sequence (U.S. Pat. No.5,487,972). This is accomplished by placing the probe adjacent to theupstream primer, on the target sequence. In this manner, sequentialrounds of annealing and subsequent probe hydrolysis can occur, resultingin a significant amount of signal generation in the absence ofpolymerization. Uses of the real-time hydrolysis probe reaction are alsodescribed in U.S. Pat. Nos. 5,538,848 and 7,205,105, both of which areincorporated by references.

6. Dye-Primer Based Systems

There are numerous dye-labeled primer based systems available forreal-time PCR. These range in complexity from simple hairpin primersystems to more complex primer structures where the stem-loop portion ofthe hairpin probe is attached via a non-amplifiable linker to thespecific PCR primer. These methods have the advantage that they do notrequire an additional intervening labeled probe that is essential forprobe-based assay systems and they also allow for multiplexing that isnot possible with DNA binding dyes. However, the success of each ofthese methods is dependent upon careful design of the primer sequences.

Hairpin primers contain inverted repeat sequences that are separated bya sequence that is complementary to the target DNA (Nazarenko et al.,1997; Nazarenko et al., 2002; U.S. Pat. No. 5,866,336). The repeatsanneal to form a hairpin structure, such that a fluorophore at the5′-end is in close proximity to a quencher at the 3′-end, quenching thefluorescent signal. The hairpin primer is designed so that it willpreferentially bind to the target DNA, rather than retain the hairpinstructure. As the PCR reaction progresses, the primer anneals to theaccumulating PCR product, the fluorophore and quencher become physicallyseparated, and the level of fluorescence increases.

Invitrogen's LUX™ (Light Upon eXtension) primers are fluorogenic hairpinprimers which contain a short 4-6 nucleotide extension at the 5′ end ofthe primer that is complementary to an internal sequence near the 3′ endand overlaps the position of a fluorophore attached near the 3′ end(Chen et al., 2004; Bustin, 2002). Basepairing between the complementarysequences forms a double-stranded stem which quenches the reporter dyethat is in close proximity at the 3′ end of the primer. During PCR, theLUX™ primer is incorporated into the new DNA strand and then becomeslinearized when a new complementary second strand is generated. Thisstructural change results in an up to 10-fold increase in thefluorescent signal. These primers can be difficult to design andsecondary structure must be carefully analyzed to ensure that the probeanneals preferentially to the PCR product. Design and validationservices for custom LUX™ primers are available from Invitrogen.

More recently, hairpin probes have become part of the PCR primer(Bustin, 2002). In this approach, once the primer is extended, thesequence within the hairpin anneals to the newly synthesized PCRproduct, disrupting the hairpin and separating the fluorophore andquencher.

Scorpion® primers are bifunctional molecules in which an upstreamhairpin probe sequence is covalently linked to a downstream primersequence (U.S. Published Application No. 2001/6270967; U.S. PublishedApplication No. 2005/0164219; Whitcombe et al., 1999). The probecontains a fluorophore at the 5′ end and a quencher at the 3′ end. Inthe absence of the target, the probe forms a 6-7 base stem, bringing thefluorophore and quencher in close proximity and allowing the quencher toabsorb the fluorescence emitted by the fluorophore. The loop portion ofthe scorpion probe section consists of sequence complementary to aportion of the target sequence within 11 bases downstream from the 3′end of the primer sequence. In the presence of the target, the probebecomes attached to the target region synthesized in the first PCRcycle. Following the second cycle of denaturation and annealing, theprobe and the target hybridize. Denaturation of the hairpin looprequires less energy than the new DNA duplex produced. Thus, thescorpion probe loop sequence hybridizes to a portion of the newlyproduced PCR product, resulting in separation of the fluorophore fromthe quencher and an increase in the fluorescence emitted.

As with all dye-primer based methods, the design of Scorpion primersfollows strict design considerations for secondary structure and primersequence to ensure that a secondary reaction will not compete with thecorrect probing event. The primer pair should be designed to give anamplicon of approximately 100-200 bp. Ideally, the primers should haveas little secondary structure as possible and should be tested forhairpin formation and secondary structures. The primer should bedesigned such that it will not hybridize to the probe element as thiswould lead to linearization and an increase in non-specific fluorescenceemission. The Tm's of the two primers should be similar and the stem Tmshould be 5-10° C. higher than the probe Tm. The probe sequence shouldbe 17-27 bases in length and the probe target should be 11 bases or lessfrom the 3′ end of the scorpion. The stem sequence should be 6 to 7bases in length and should contain primarily cytosine and guanine. The5′ stem sequence should begin with a cytosine as guanine may quench thefluorophore. Several oligonucleotide design software packages containalgorithms for Scorpion primer design and custom design services areavailable from some oligonucleotide vendors as well.

The Plexor™ system from Promega is a real-time PCR technology that hasthe advantage that there are no probes to design and only one PCR primeris labeled (U.S. Pat. No. 5,432,272; U.S. Published Application No.2000/6140496; U.S. Published Application No. 2003/6617106). Thistechnology takes advantage of the specific interaction between twomodified nucleotides, isoguanine (iso-dG) and 5′-methylisocytosine(iso-dC) (Sherrill et al., 2004; Johnson et al., 2004; Moser andPrudent, 2003). Main features of this technology are that the iso-baseswill only base pair with the complementary iso-base and DNA polymerasewill only incorporate an iso-base when the corresponding complementaryiso-base is present in the existing sequence. One PCR primer issynthesized with a fluorescently-labeled iso-dC residue as the5′-terminal nucleotide. As amplification progresses, the labeled primeris annealed and extended, becoming incorporated in the PCR product. Aquencher-labeled iso-dGTP (dabsyl-iso-dGTP), available as the freenucleotide in the PCR master mix, specifically base pairs with theiso-dC and becomes incorporated in the complementary PCR strand,quenching the fluorescent signal. Primer design for the Plexor system isrelatively simple as compared to some of the other dye-primer systemsand usually follows typical target-specific primer designconsiderations. A web-based Plexor Primer Design Software, availablefrom Promega, assists in selecting the appropriate dye and quenchercombinations, and provides links to oligonucleotide suppliers licensedto provide iso-base containing primers.

D. Exemplary Chemistries

As discussed above, there are several commercially available nucleicacid detection chemistries currently used in real-time PCR. Currentreal-time PCR technologies are, however, limited in their multiplexingcapabilities to reactions of about 1-6 plex. The methods and systems ofthe present invention can achieve far greater real-time PCR multiplexingusing commercially available nucleic acid detection chemistries,including detection chemistries not previously used for real-time PCR.Embodiments describing the use of several of these detection chemistriesin the context of the present invention are discussed below.

1. Molecular Beacons

Molecular beacons, also known as hairpin probes, can be described asstem-loop structures that open and hybridize in the presence of acomplementary target sequence, typically causing an increase influorescence but in the absence thereof, form a stem-loop structureresulting in decreased fluorescence (U.S. Pat. No. 5,925,517; U.S.Published Application No. 2006/103476). Probes according to oneembodiment of the present invention are labeled probes that have anucleic acid target complement sequence flanked by members of anaffinity pair, or arms, that, under assay conditions in the absence oftarget, interact with one another to form a stem duplex. Hybridizationof the probes to their preselected target sequences produces aconformational change in the probes, forcing the arms apart andeliminating the stem duplex. Embodiments of probes according to thisinvention employ interactive labels, whereby that conformational changecan be detected, or employ a specially limited allele-discriminatingstructure, or both. A characteristic change in signal level depends onwhether the label moieties are proximate due to the probes being in theclosed position or are separated due to the probes being in the openposition. According to this embodiment, molecular beacons are also boundto a spectrally or otherwise distinguishable particle, which providesfor higher levels of multiplexing than were previously possible by usingconventional methods wherein the dyes attached to the hairpin probes bydistinguishing the color of the dye rather than the distinguishingproperties of the particle attached to the capture probe.

FIGS. 5 and 6 illustrate how one embodiment of the present invention canseparate the fluorochrome from the quenching molecule allowing fordetectable fluorescence on the surface of a particle. In FIG. 5, hairpinprobes coupled to a quenching molecule and a fluorochrome arehomogeneous in solution. Quenching molecule 200 limits the amount offluorescence emitted by the fluorochrome molecule 202 when the probe isin the hairpin formation. The oligonucleotide probe in the hairpinformation is denoted as 205 in FIG. 5. When the inner loop of thehairpin molecule hybridizes to a target amplicon, the fluorochrome andthe quenching molecule are separated as illustrated in FIGS. 5 and 6allowing for detectable fluorescence on the surface of the bead 40. Toimage this fluorescence, the beads 40 are pulled to the planar array bymoving magnetic element 264 proximate to the array and detecting thefluorescence with an imaging system, such as the imaging systemsillustrated in FIGS. 1-2, and 9.

2. Hybridization Probes

Hybridization probes used in real-time PCR are sometimes referred to asFRET probes, LightCycler® probes, or dual FRET probes (Espy et al.,2006). Hybridization probes are used in a format in which FRET ismeasured directly (Wilhelm and Pingoud, 2003). Each of the two probes islabeled with a respective member of a fluorescent energy transfer pair,such that upon hybridization to adjacent regions of the target DNAsequence, the excitation energy is transferred from the donor to theacceptor, and subsequent emission by the acceptor can be recorded asreporter signal (Wittwer et al., 1997). The two probes anneal to thetarget sequence so that the upstream probe is fluorescently labeled atits 3′ end and the downstream probe is labeled at its 5′ end. The 3′ endof the downstream probe is typically blocked by phosphorylation or someother means to prevent extension of the probe during PCR. The dyecoupled to the 3′ end of the upstream probe is sufficient to preventextension of this probe.

In this embodiment one of two of the hybridization probes can be coupledto the distinguishable particles (e.g., encoded beads). In this instancethe capture probe coupled to the particle will be complimentary to thetarget nucleic acid sequence of interest and the uncoupled probe willhybridize to an adjacent region along the target sequence. In thecontext of a real-time PCR reaction, the target sequence is theamplicon. Either the donor or the acceptor fluorophores can be attachedto the oligonucleotide sequence that is attached to the particle.

Typical acceptor fluorophores include the cyanine dyes (Cy3 and Cy5),6-carboxy-4,7,2′,7′-tetrachlorofluorescein (TET),6-carboxy-N,N,N′,N′-tetramethylrhodamine (TAMRA), and 6-carboxyrhodamineX (ROX). Donor fluorophores are usually 6-carboxyfluoroscein (FAM)(Wilhelm and Pingoud, 2003). Genotyping of the target sequence isaccomplished by matching the reporter probes to their correspondingsequences.

FIG. 7 illustrates a modified FRET (Fluorescence Resonance EnergyTransfer) hybridization probe in the context of the present invention.Donor fluorophore 210 is attached to the probe immobilized on thesurface of paramagnetic microsphere 40. Upon reaching the detectionphase of each PCR cycle, the temperature of the solution will beconducive to hybridization of both the donor-labeled probe andacceptor-labeled probe to the target sequence. The close proximity ofthe donor 210 and acceptor 212 pair will allow for FluorescenceResonance Energy Transfer. This will result in fluorescence only nearthe surface of the bead 40, by allowing the acceptor molecule 212 toemit light at a different wavelength than the donor 210.

Thus, in one embodiment of performing a method for multiplexed,real-time amplification and detection of a plurality of nucleic acidtargets in a sample using FRET hybridization probes, one would combinein a chamber a sample comprising the plurality of nucleic acid targets,a plurality of primer pairs for priming amplification of the pluralityof nucleic acid targets, and a plurality of probe sets complementary tothe plurality of nucleic acid targets, wherein each probe set comprisesa first probe labeled with a first member of a fluorescent energytransfer pair and immobilized on an encoded magnetic bead such that theidentity of the first probe is known from the encoded magnetic bead onwhich it is immobilized, and a second probe with a second member of thefluorescent energy transfer pair. One would then perform anamplification cycle to form amplification products for each of theplurality of nucleic acid targets amplified with the plurality of primerpairs. The amplification products would be hybridized to the probe sets.By applying a magnetic field to a surface of the chamber the encodedmagnetic beads and the amplification products hybridized to the probesimmobilized on the encoded magnetic beads are drawn to the surface ofthe chamber, where an imaging system, such as those described elsewhereherein, detects a signal from the encoded magnetic beads and a signalfrom the fluorescent energy transfer pair hybridized to theamplification products. The magnetic field may then removed from thesurface of the chamber in order to performing a further amplificationcycle. The amplification and detection may be repeated the desirednumber of times to obtain real-time quantitative data on the reaction.It should be noted that the signal from the fluorescent energy transferpair may be an increase in fluorescence or a decrease in fluorescencedepending on the reporter molecules employed.

This two probe system may also be used without a FRET pair. In thisembodiment only the probe that is not coupled to the particle islabeled, and therefore the hybridization of both probes to the targetsequence is detectable by virtue of the label on one of the two probes.For example, one would combine in a chamber a sample comprising aplurality of nucleic acid targets, a plurality of primer pairs forpriming amplification of the plurality of nucleic acid targets, and aplurality of probe sets complementary to the plurality of nucleic acidtargets, wherein each probe set comprises a first probe immobilized onan encoded magnetic bead such that the identity of the first probe isknown from the encoded magnetic bead on which it is immobilized, and asecond probe comprising a label. An amplification cycle is performed toform amplification products for each of the plurality of nucleic acidtargets amplified with the plurality of primer pairs. The amplificationproducts are hybridized to the probe sets, and a magnetic field isapplied to a surface of the chamber to draw the encoded magnetic beadsand the amplification products hybridized to the probes immobilized onthe encoded magnetic beads to the surface of the chamber. Thenon-immobilized, labeled probe would also be pulled to the surface ofthe chamber because it is hybridized to a complementary sequence on theamplification product. An imaging system, such as those describedelsewhere herein, may then be used to detect a signal from the encodedmagnetic beads and a signal from the second probe hybridized to theamplification products. The magnetic field may then be removed from thesurface of the chamber prior to performing a further amplificationcycle. The amplification and detection may be repeated the desirednumber of times to obtain real-time quantitative data on the reaction.

Additional free floating FRET dyes or other reporter molecules which areattached to probes (e.g., a third probe, fourth probe, etc. of a probeset) may be included in certain embodiments, wherein more than one pairof probes is allowed to hybridize to the target nucleic acid sequence atany given time so long as one probe of the probe set is coupled to aparticle or magnetic encoded particle. These additional probes canfurther increase the sensitivity, specificity, and multiplexing abilityof the method by adding additional distinguishing features or additionalreporter molecules which are attached to the target. For example, byhaving a probe which is coupled to a magnetic encoded particle, thatprobe may hybridize to a target which is longer than the probe, suchthat other probes which are modified with other reporter molecules mayhybridize to a region of the target sequence that is either 5′ or 3′ tothe probe that is coupled to the magnetic encoded particle.

Additional reagents may be used to improve the efficiency of any of theembodiments described herein. These reagents may improve the methods byusing PCR additives that are known to those skilled in the art. BSA orother molecules which act as blocking agents or detergents orsurfactants may also improve the methods described herein. BSA or othersimilar reagents known to those skilled in the art may improve a PCRreaction performed in a glass or quartz chamber by reducing theattraction of DNA and other reagents to the surfaces of the reactionchamber. Other additives may be used which exhibit molecular crowdingeffects to improve the time to hybridization. Other molecules, reagents,chemicals, solutions known to those skilled in the art which may improvethe time to hybridization may also be used. An example of such may benucleic acid binding proteins or minor groove binders.

Those skilled in the art will recognize that modifications to thereporter dye, such as the well-known method of adding sulfate groups,will alter the hydrophilicity of the dye molecules, which may lead toless non-specific binding to the encoded magnetic particles.

3. Two Probe Competition

Other embodiments employ the use of two probes per target nucleic acidsequence. One probe is attached to a bead and may be labeled with afluorophore. A complimentary “free-floating” probe is also added thatcontains either a quencher or a fluorophore pair such that FRET mayoccur. In this instance, the probe on the bead may contain a fluorophoreat the 3′ end, while being attached to the bead at the 5′ end. Thefree-floating probe will be able to quench the signal associated withthe fluorophore on the bead by being designed as a reverse compliment ofthe same, and having a quenching moiety at its 5′ end, such that it isin close proximity to the fluorophore, and therefore achieves a decreasein signal upon hybridization to the probe. These probes will also bepresent during PCR amplification or some other amplification event. Atthe target detection phase of the PCR cycle, the free-floating probewill leave the probe attached to the bead and will hybridize to thetarget sequence. The probe attached to the bead will be designed suchthat it exhibits less favorable binding as well as a lower meltingtemperature with the free-floating probe, compared to the free-floatingprobe with the target sequence. As the target sequence increases inconcentration, as the PCR reaction continues, a significant increase insignal associated with the beads may be observed. The same effect of ameasurable increase in signal may be obtained by a similar method ofdesigning the probe that is attached to the bead to exhibit favorablebinding of the target sequence compared to the binding kinetics of thetarget sequence with the free-floating probe. Differences in bindingkinetics may be obtained by designing the free-floating and the fixedprobe to be of differing lengths with respect to one another, or byinserting a base or more than one base on one of the probes that is amismatch with respect to the sequence on the other probe but not withrespect to the target sequence.

4. Incorporated Quenching Molecules

FIG. 8 illustrates an example in which quenching molecules areincorporated into a newly synthesized DNA strand by pre-couplingnucleotides to quenching molecules. This the pre-couplednucleotide/quencher will be available in the PCR reaction mix and willbe incorporated into the amplification products. A complementary probelabeled with a fluorochrome attached to the surface of the bead 40 willresult in a system in which fluorescent signal decreases as more andmore of the target oligonucleotides sequence is produced. For example,one could combine in a chamber a sample comprising the plurality ofnucleic acid targets, a plurality of primer pairs for primingamplification of the plurality of nucleic acid targets, a mixture ofdNTPs in which a portion of the dNTPs are coupled to quencher molecules,and a plurality of fluorescently labeled probes complementary to theplurality of nucleic acid targets, wherein the probes are immobilized ona plurality of encoded magnetic beads such that the identity of eachprobe is known from the encoded magnetic bead on which it isimmobilized. An amplification cycle is performed to form amplificationproducts for each of the plurality of nucleic acid targets amplifiedwith the plurality of primer pairs. Because a portion of the dNTPs inthe amplification reaction are coupled to quencher molecules, theamplification products will incorporate these quencher molecules. Theamplification products are then hybridized to the probes immobilized onthe encoded magnetic beads, and a magnetic field is applied to a surfaceof the chamber to draw the encoded magnetic beads and the amplificationproducts hybridized to the probes immobilized on the encoded magneticbeads to the surface of the chamber. Signals from the encoded magneticbeads and signals from the labeled probes are then detected. Because theamplification products incorporate quencher molecules, the fluorescentsignal from the probes decreases as more and more of the amplificationproduct is produced. The magnetic field may be removed from the surfaceof the chamber prior to performing a further amplification cycle. Theamplification and detection may be repeated the desired number of timesto obtain real-time quantitative data on the reaction.

5. Direct Hybridization

PCR may be performed wherein the primers used to form amplifiedsequences or amplicons are labeled with a fluorochrome (e.g., Cy3) orother substance that allows for detection. Labeling may be at, forexample, the 5-prime end of the primer. Using primers that are labeledallows formation of labeled amplicons. The amplified nucleic acidsequences that are labeled may hybridize to and be captured byoligonucleotide probes that are coupled to the distinguishableparticles. No current, commercial real-time PCR methods employ the useof direct hybridization methods.

An embodiment using a direct hybridization approach is illustrated inFIG. 11. As shown in FIG. 11, one primer of a primer pair is labeled atits 5′ end with a reporter molecule such as the fluorophore Cy3. Theprimer pair amplifies a target sequence from the sample DNA present inthe PCR to form a labeled amplicon. Also present in the PCR is amagnetic, encoded bead coupled to a probe that is complementary to thelabeled strand of the amplicon. The 3′ end of the immobilized probe maybe blocked (with a phosphate group or a 3′ inverted dT, for example) toprevent the polymerase extension of the probe. After the desired numberof PCR cycles, a magnetic field is applied to the chamber to pull themagnetic, encoded beads to a surface of the chamber for detection. Thisstep is performed under hybridization conditions such that labeledamplicons will hybridize to their complementary probes and as such, willbe also be pulled to a surface of the chamber. The presence of thelabeled amplicons is detected by the detection of the label (e.g. afluorescent signal from a Cy3 label) at the surface of chamber.Although, the FIG. 11 illustrates a single-plex reaction, it is to beunderstood that this method can be applied to multiplex PCR reactions aswell. The encoded beads, the labels on the amplicons, and combinationsthereof, can be used to distinguish large numbers of different ampliconsin the same reaction.

6. Tagged Primers

In another embodiment, the present invention provides a method ofamplifying and detecting a plurality of nucleic acid targets in a samplecomprising combining in a chamber a sample comprising the plurality ofnucleic acid targets; a plurality of primer pairs for primingamplification of the plurality of nucleic acid targets, wherein eachprimer pair comprises a first primer comprising a target specificsequence, a tag sequence 5′ of the target specific sequence, and ablocker between the target specific sequence and the tag sequence, and asecond primer comprising a target specific sequence; a labeling agent;and a plurality of probes (anti-tags) complementary to the tag sequencesof the plurality of primer pairs, wherein the probes are immobilized ona plurality of encoded magnetic beads such that the identity of eachprobe is known from the encoded magnetic bead on which it isimmobilized. An amplification cycle is performed to form tagged andlabeled amplification products for each of the plurality of nucleic acidtargets amplified with the plurality of primer pairs. The tagged andlabeled amplification products are hybridized to the probes immobilizedon the encoded magnetic beads, and a magnetic field is applied to asurface of the chamber to draw the encoded magnetic beads and the taggedand labeled amplification products hybridized to the probes immobilizedon the encoded magnetic beads to the surface of the chamber. Signalsfrom the encoded magnetic beads and signals from the tagged and labeledamplification products are then detected using, for example, an imagingsystem such as those described herein. The magnetic field may be removedfrom the surface of the chamber prior to performing a furtheramplification cycle. The amplification and detection may be repeated thedesired number of times to obtain real-time quantitative data on thereaction. In certain aspects, the labeling agent may be a reportermolecule attached to the second primer of the primer pair. In otheraspects, the labeling agent may be an intercalating dye.

As mentioned above, complementary tag sequences (i.e., tags andanti-tags) may be used in the primers and probes. A number of approacheshave been developed that involve the use of oligonucleotide tagsattached to a solid support that can be used to specifically hybridizeto the tag complements that are coupled to primers, probe sequences,target sequences, etc. The proper selection of non-hybridizing tag andanti-tag sequences is useful in assays, particularly assays in a highlyparallel hybridization environment, that require stringent non-crosshybridizing behavior.

Certain thermodynamic properties of forming nucleic acid hybrids areconsidered in the design of tag and anti-tag sequences. The temperatureat which oligonucleotides form duplexes with their complementarysequences known as the T_(m) (the temperature at which 50% of thenucleic acid duplex is dissociated) varies according to a number ofsequence dependent properties including the hydrogen bonding energies ofthe canonical pairs A-T and G-C (reflected in GC or base composition),stacking free energy and, to a lesser extent, nearest neighborinteractions. These energies vary widely among oligonucleotides that aretypically used in hybridization assays. For example, hybridization oftwo probe sequences composed of 24 nucleotides, one with a 40% GCcontent and the other with a 60% GC content, with its complementarytarget under standard conditions theoretically may have a 10° C.difference in melting temperature (Mueller et al., 1993). Problems inhybridization occur when the hybrids are allowed to form underhybridization conditions that include a single hybridization temperaturethat is not optimal for correct hybridization of all oligonucleotidesequences of a set. Mismatch hybridization of non-complementary probescan occur, forming duplexes with measurable mismatch stability(Santalucia et al., 1999). Mismatching of duplexes in a particular setof oligonucleotides can occur under hybridization conditions where themismatch results in a decrease in duplex stability that results in ahigher T_(m) than the least stable correct duplex of that particularset. For example, if hybridization is carried out under conditions thatfavor the AT-rich perfect match duplex sequence, the possibility existsfor hybridizing a GC-rich duplex sequence that contains a mismatchedbase having a melting temperature that is still above the correctlyformed AT-rich duplex. Therefore, design of families of oligonucleotidesequences that can be used in multiplexed hybridization reactions mustinclude consideration for the thermodynamic properties ofoligonucleotides and duplex formation that will reduce or eliminatecross hybridization behavior within the designed oligonucleotide set.

There are a number of different approaches for selecting tag andanti-tag sequences for use in multiplexed hybridization assays. Theselection of sequences that can be used as zip codes or tags in anaddressable array has been described in the patent literature in anapproach taken by Brenner and co-workers (U.S. Pat. No. 5,654,413,incorporated herein by reference). Chetverin et al (WO 93/17126, U.S.Pat. Nos. 6,103,463 and 6,322,971, incorporated herein by reference)discloses sectioned, binary oligonucleotide arrays to sort and surveynucleic acids. These arrays have a constant nucleotide sequence attachedto an adjacent variable nucleotide sequence, both bound to a solidsupport by a covalent linking moiety. Parameters used in the design oftags based on subunits are discussed in Barany et al. (WO 9731256,incorporated herein by reference). A multiplex sequencing method hasbeen described in U.S. Pat. No. 4,942,124, incorporated herein byreference. This method uses at least two vectors that differ from eachother at a tag sequence.

U.S. Pat. No. 7,226,737, incorporated herein by reference, describes aset of 210 non-cross hybridizing tags and anti-tags. U.S. PublishedApplication No. 2005/0191625, incorporated herein by reference,discloses a family of 1168 tag sequences with a demonstrated ability tocorrectly hybridize to their complementary sequences with minimal crosshybridization. U.S. Application No. 60/984,982, incorporated herein byreference, describes the use of tags, anti-tags, and capture complexesin the amplification of nucleic acid sequences.

A population of oligonucleotide tag or anti-tag sequences may beconjugated to a population of primers or other polynucleotide sequencesin several different ways including, but not limited to, direct chemicalsynthesis, chemical coupling, ligation, amplification, and the like.Sequence tags that have been synthesized with target specific primersequences can be used for enzymatic extension of the primer on thetarget for example in PCR amplification. A population of oligonucleotidetag or anti-tag sequences may be conjugated to a solid support by, forexample, surface chemistries on the surface of the support.

As discussed above, one primer of a primer pair used in an amplificationreaction comprises a tag sequence. Following the initial extension ofthe primer comprising the tag sequence, the tagged extension product mayserve as a template for the other primer of the primer pair. It would beundesirable, however, for the extension on such a template to proceedthrough the tag region as this could interfere with the hybridization ofthe tag sequence with the anti-tag sequence of the probe. Accordingly, ablocker may be positioned between the target specific sequence and thetag sequence of the primer. Blocker moieties prevent the polymerase fromextending into the tag sequence region, which allows the tag sequence toremain single-stranded during amplification and therefore free tohybridize to its complementary anti-tag sequence in the capture complex.

A blocker moiety refers to any moiety that when linked (e.g., covalentlylinked) between a first nucleotide sequence and a second nucleotidesequence is effective to inhibit and preferably prevent extension ofeither the first or second nucleotide sequence but not both the firstand second nucleotide sequence. There are a number of molecules that maybe used as blocker moieties. Non-limiting examples of blocker moietiesinclude C6-20 straight chain alkylenes and iSp18 (which is an 18-atomhexa-ethyleneglycol). Blocker moieties may include, for example, atleast one deoxy ribofuranosyl naphthalene or ribofuranosyl naphthalenemoiety, which may be linked to the adjacent nucleotides via a3′-furanosyl linkage or preferably via a 2′-furanosyl linkage. A blockermoiety may be an oligonucleotide sequence that is in the oppositeorientation as the target specific sequence. Accordingly, in certainaspects of the invention a primer's tag sequence may be both the tag andthe blocker, where the target specific sequence is in the 5′ to 3′orientation but the tag sequence is in the 3′ to 5′ orientation. In thisorientation the tag sequence is not extendable by the polymerase enzyme.Various blocker moieties and their use are described in U.S. Pat. No.5,525,494, which is incorporated herein by reference.

If a blocker moiety is not used, steps may be taken to permit thehybridization of the tag sequence with the anti-tag sequence. Forexample, an anti-tagged primer may be substituted for the tagged andblocked primer in the amplification. In which case, the polymerase isallowed to extend into the anti-tag sequence region, creating thecomplementary tag sequence. The double-stranded amplification productwhich contains an anti-tag/tag region is then denatured prior tohybridization to the anti-tag coupled to the solid substrate.

7. Primers Attached to Particles

In certain embodiments of the invention, primers that are themselvesattached to the surface of the magnetically responsive particle may beused. In such embodiments, hybridization probes attached to the beadswould not be required to capture the amplicons since the amplicons wouldbe synthesized on the beads. Typically, only one primer of each primerpair would be attached to the particle. The other primer of the primerpair would be “free floating.” Such primers may also exhibit propertiesthat allow them to be spectrally distinguishable upon extension, such aswith primers that also act as molecular beacons, whereupon a change insignal is observed upon extension of the primer which changes theproximity of a fluorophore and quencher. Other detection chemistries,such as labeling the free-floating primer, incorporating labeled dNTPsinto the amplicon, or using DNA intercalating agents, may also be usedwith these embodiments.

8. Hydrolysis Probes

Another method of target nucleic acid detection takes advantage of theexonuclease activity of some polymerases. In this embodiment, afluorophore and quencher pair, or a FRET pair may be modifications of asingle probe that is attached to a particle (e.g., a bead). One of thesefluorochromes may also be attached to the surface of the magnetic bead,with the other fluorochrome being attached to the probe which is affixedto the surface of the particle, such that both fluorochromes interact byvirtue of their close spatial proximity to one another. Uponhybridization of the target sequence to the probe, another primer islocated downstream of the probe such that upon extension of the primer,the quenching moiety (or fluorescent moiety) is cleaved, yielding ameasurable change in signal.

9. SimpleProbes®

Other embodiments may incorporate the use of SimpleProbes® or probesthat are equivalent to SimpleProbes®, which are attached to beads forthe purpose of viewing data in real-time. These probes are described inU.S. Pat. No. 6,635,427. SimpleProbes® may be attached tosuperparamagnetic microspheres using an amino modified C12 linker or bysome other linker, or another covalent binding interaction. By attachingthese probes to beads, the beads may be present during the PCR reaction,such that by binding to the intended target sequences, a double-strandedproduct is formed, allowing detection and analysis of the nucleic acidsequences in a highly multiplexed real-time PCR format.

10. Immuno-PCR

Immuno-PCR may be used to detect an antigen, cell, endospore, or anyother molecule or protein of interest that can be detected by anantibody wherein said antibody is linked to a nucleic acid sequence.Existing methods of immuno-PCR are disclosed in U.S. Pat. No. 5,665,539;Sano, T. et al., Science, 258:120-122 (1992); and Sims, P W et al., AnalBiochem. 281:230-232 (2000), each of which is incorporated by reference.Existing methods, however, are limited in multiplexing ability to detectImmuno-PCR in real-time. In one embodiment, the present inventionprovides a method that can greatly increases the multiplexing ability todetect Immuno-PCR in real-time by first linking capture antibodies oraptamers to a particle that is magnetic (e.g., superparamagnetic) innature, wherein the particle is able to react and bind to the targetmolecule of interest. This particle need not be encoded to be spectrallyidentifiable. After reaction occurs, or during the reaction, or prior tothe reaction, the magnetic particles, which can be nanoparticles ormicroparticles, may be brought into the detection and amplificationchamber. The particles, which are linked to the capture antibodies oraptamers, may be drawn to the surface of the chamber by applying amagnetic field. These particles and the molecules bound or otherwiseattached thereto, may undergo a washing procedure, which may includeflowing a volume of aqueous solution over the particles, which are heldin place by magnetic forces, washing away excess target molecule if needbe.

A detection antibody or detection aptamer may be introduced into thereaction chamber and allowed to react and bind to the target molecule,which is also bound by the capture antibody or aptamer, which is in turnlinked to the magnetic particles. The detection antibody or detectionaptamer is linked to a nucleic acid sequence, which is capable offorming an amplifiable nucleic acid product. The detection antibody neednot be introduced while in the detection chamber which is capable ofapplication of a magnetic field, but may be introduced in a separatereaction vessel, and then subsequently introduced into the reactionvessel which is capable of application of a magnetic field. Thedetection antibody need not be introduced with the target molecule orthe target/capture/particle complex prior to a wash procedure. Once thetarget/capture/particle complex or target/capture/particle/detectioncomplex (capture sandwich complex) is introduced into the detectionchamber which is capable of application of a magnetic field, thiscomplex may be drawn to the surface of the chamber, if the particleshave not already been drawn to the surface of the chamber in any numberof various derivations of methods of forming or washing thetarget/capture/particle complex, or any parts thereof which have notbeen fully complexed. Once drawn to the surface of the chamber, thiscomplex may be washed by any number of reagents or buffers or aqueoussolutions known in the art for accomplishing such. Buffers that maycommonly be used may include but are not limited by using PBS, BSA,PBS/BSA, water, PCR buffer, etc. Washing in this instance may improvethe assay by removing excess detection antibody or aptamer, which mayincrease specificity. The capture antibody or capture aptamer, need notbe attached to a particle capable of being drawn to a surface if washingis not desired.

The capture sandwich complex may be used in a PCR reaction or real-timePCR reaction wherein encoded magnetic beads are also present. In thisembodiment, the capture sandwich complex or plurality of capturesandwich complexes would have been introduced into a detection chamberwhich is capable of thermal cycling, having been drawn and held to asurface of the chamber by a magnetic field in order to perform a washingprocedure. After washing, the encoded beads, which are coupled withnucleic acid probes suitable for nucleic acid target detection would beintroduced thereto in a medium also comprising all the reagents andcomponents necessary to perform a Polymerase Chain Reaction or othermethod of nucleic acid amplification. The solution would also containany number of reagents necessary for multiplexed detection of real-timePCR as described in other embodiments herein. For example, the pluralityof detection antibodies or detection aptamers are linked to nucleic acidsequences which are comprised of different combinations of sequences soas to allow multiplexed detection of the nucleic acid sequences suchthat detection of such plurality of sequences could be related back tothe detection or quantification of the target molecule by virtue of itsassociation with the detection antibody or detection aptamer.

For example, once that capture sandwich complex and PCR reagents as wellas encoded magnetic beads have been combined the subsequent methods mayinclude any number of embodiments for multiplexed amplification anddetection described herein. For example, In one embodiment, the presentinvention provides a method of amplifying and detecting a plurality ofnucleic acid targets in a sample comprising: (a) combining in a chambera sample comprising the plurality of nucleic acid targets, a pluralityof primer pairs for priming amplification of the plurality of nucleicacid targets, a labeling agent, and a plurality of probes complementaryto the plurality of nucleic acid targets, wherein the probes areimmobilized on a plurality of encoded magnetic beads such that theidentity of each probe is known from the encoded magnetic bead on whichit is immobilized; (b) performing an amplification cycle to form labeledamplification products for each of the plurality of nucleic acid targetsamplified with the plurality of primer pairs; (c) hybridizing thelabeled amplification products to the probes immobilized on the encodedmagnetic beads; (d) applying a magnetic field to a surface of thechamber to draw the encoded magnetic beads and the labeled amplificationproducts hybridized to the probes immobilized on the encoded magneticbeads to the surface of the chamber; (e) detecting the encoded magneticbeads and the labeled amplification products; (f) removing the magneticfield from the surface of the chamber prior to performing a furtheramplification cycle; and (g) repeating steps (b) through (f) at leastonce; wherein the plurality of nucleic acid targets in the sample areamplified and detected. In certain aspects of the invention, steps (b)through (f) are repeated between 10 to 40 times.

11. Nucleic Acid Analogs

The nucleic acids used in the methods disclosed herein may includenucleotide isomers or base analogs such as “Locked Nucleic Acids” orothers. A nucleic acid sequence may comprise, or be composed entirelyof, an analog of a naturally occurring nucleotide. Nucleotide analogsare well known in the art. A non-limiting example is a “peptide nucleicacid,” also known as a “PNA,” “peptide-based nucleic acid analog,” or“PENAM,” described in U.S. Pat. Nos. 5,786,461, 5,891,625, 5,773,571,5,766,855, 5,736,336, 5,719,262, 5,714,331, 5,539,082, and WO 92/20702,each of which is incorporated herein by reference. Peptide nucleic acidsgenerally have enhanced sequence specificity, binding properties, andresistance to enzymatic degradation in comparison to molecules such asDNA and RNA (Egholm et al., 1993; PCT/EP/01219). A peptide nucleic acidgenerally comprises one or more nucleotides or nucleosides that comprisea nucleobase moiety, a nucleobase linker moiety that is not a 5-carbonsugar, and/or a backbone moiety that is not a phosphate backbone moiety.Examples of nucleobase linker moieties described for PNAs include azanitrogen atoms, amido and/or ureido tethers (see for example, U.S. Pat.No. 5,539,082). Examples of backbone moieties described for PNAs includean aminoethylglycine, polyamide, polyethyl, polythioamide,polysulfinamide or polysulfonamide backbone moiety.

Another non-limiting example is a locked nucleic acid or “LNA.” An LNAmonomer is a bi-cyclic compound that is structurally similar to RNAnucleosides. LNAs have a furanose conformation that is restricted by amethylene linker that connects the 2′-O position to the 4′-C position,as described in Koshkin et al., 1998a and 1998b and Wahlestedt et al.,2000.

Yet another non-limiting example is a “polyether nucleic acid,”described in U.S. Pat. No. 5,908,845, incorporated herein by reference.In a polyether nucleic acid, one or more nucleobases are linked tochiral carbon atoms in a polyether backbone.

12. Hybridization

As used herein, “hybridization,” “hybridizes” or “capable ofhybridizing” is understood to mean the forming of a double or triplestranded molecule or a molecule with partial double or triple strandednature. The term “anneal” as used herein is synonymous with “hybridize.”The term “hybridization,” “hybridizes” or “capable of hybridizing”encompasses the terms “stringent conditions” or “high stringency” andthe terms “low stringency” or “low stringency conditions.”

As used herein “stringent conditions” or “high stringency” are thoseconditions that allow hybridization between or within one or morenucleic acid strands containing complementary sequences, but precludehybridization of non-complementary sequences. Such conditions are wellknown to those of ordinary skill in the art, and are preferred forapplications requiring high selectivity. Stringent conditions maycomprise low salt and/or high temperature conditions, such as providedby about 0.02 M to about 0.15 M NaCl at temperatures of about 50° C. toabout 70° C. It is understood that the temperature and ionic strength ofa desired stringency are determined in part by the length of theparticular nucleic acids, the length and nucleobase content of thetarget sequences, the charge composition of the nucleic acids, and tothe presence or concentration of formamide, tetramethylammonium chlorideor other solvents in a hybridization mixture.

It is also understood that these ranges, compositions and conditions forhybridization are mentioned by way of non-limiting examples only, andthat the desired stringency for a particular hybridization reaction isoften determined empirically by comparison to one or more positive ornegative controls. Non-limiting examples of low stringency conditionsinclude hybridization performed at about 0.15 M to about 0.9 M NaCl at atemperature range of about 20° C. to about 50° C. Of course, it iswithin the skill of one in the art to further modify the low or highstringency conditions to suite a particular application.

E. Encoded Particles

Although certain embodiments are described herein with respect toencoded microspheres (i.e., beads), it is to be understood that theillumination subsystems, systems, and methods may also be used withother particles such as microparticles, gold or other metalnanoparticles, quantum dots, or nanodots. The particles are preferablysuper paramagnetic. Examples of microspheres, beads, and particles areillustrated in U.S. Pat. No. 5,736,330 to Fulton, U.S. Pat. No.5,981,180 to Chandler et al., U.S. Pat. No. 6,057,107 to Fulton, U.S.Pat. No. 6,268,222 to Chandler et al., U.S. Pat. No. 6,449,562 toChandler et al., U.S. Pat. No. 6,514,295 to Chandler et al., U.S. Pat.No. 6,524,793 to Chandler et al., and U.S. Pat. No. 6,528,165 toChandler, which are incorporated by reference herein.

Excitation of dyes or fluorochromes within or on the surface of encodedparticles may be accomplished by laser light, diode light, arc lamp,heat, radioactive emission, chemiluminescence, electroluminescence,chemielectroluminescence, or any other method known to those skilled inthe art.

In certain embodiments, the present invention is used in conjunctionwith Luminex® xMAP® and MagPlex™ technologies. The Luminex xMAPtechnology allows the detection of nucleic acid products immobilized onfluorescently encoded microspheres. By dyeing microspheres with 10different intensities of each of two spectrally distinct fluorochromes,100 fluorescently distinct populations of microspheres are produced.These individual populations (sets) can represent individual detectionsequences and the magnitude of hybridization on each set can be detectedindividually. The magnitude of the hybridization reaction is measuredusing a third reporter, which is typically a third spectrally distinctfluorophore. The reporter molecule signals the extent of the reaction byattaching to the molecules on the microspheres. As both the microspheresand the reporter molecules are labeled, digital signal processing allowsthe translation of signals into real-time, quantitative data for eachreaction. The Luminex technology is described, for example, in U.S. Pat.Nos. 5,736,330, 5,981,180, and 6,057,107, all of which are specificallyincorporated by reference. Luminex® MagPlex™ microspheres aresuperparamagnetic microspheres that are fluorescently encoded using thexMAP® technology discussed above. The microspheres contain surfacecarboxyl groups for covalent attachment of ligands (or biomolecules).

F. Kits

The present invention also provides kits containing components for usewith the amplification and detection methods disclosed herein. Any ofthe components disclosed here in may be combined in a kit. In certainembodiments the kits comprise a plurality of primer pairs for primingamplification of a plurality of nucleic acid targets, and a plurality ofprobes complementary to the plurality of nucleic acid targets, whereinthe probes are immobilized on a plurality of encoded magnetic beads suchthat the identity of each probe is known from the encoded magnetic beadon which it is immobilized. In certain embodiments, the kit alsocomprises a labeling agent. In certain embodiments the kits compriseprobes that are not attached to encoded magnetic beads. In someembodiments the kit comprises an imaging chamber, which may be adisposable imaging chamber, for use in an imaging system.

The components of the kits may be packaged either in aqueous media or inlyophilized form. The container means of the kits will generally includeat least one vial, test tube, flask, bottle, syringe or other containermeans, into which a component may be placed, and preferably, suitablyaliquoted. Where there is more than one component in the kit, the kitalso will generally contain a second, third or other additionalcontainers into which the additional components may be separatelyplaced. However, various combinations of components may be comprised ina vial. The kits of the present invention also will typically includepackaging for containing the various containers in close confinement forcommercial sale. Such packaging may include cardboard or injection orblow molded plastic packaging into which the desired vials, bottles,etc. are retained.

When the components of the kit are provided in one or more liquidsolutions, the liquid solution may be an aqueous solution, with asterile aqueous solution being particularly preferred. However, certaincomponents of the kit may be provided as dried powder(s). When reagentsand/or components are provided as a dry powder, the powder can bereconstituted by the addition of a suitable solvent. It is envisionedthat the solvent may also be provided in another container means.

A kit may also include instructions for employing the kit components.Instructions may include variations that can be implemented.

G. EXAMPLES

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples which follow representtechniques discovered by the inventor to function well in the practiceof the invention, and thus can be considered to constitute preferredmodes for its practice. However, those of skill in the art should, inlight of the present disclosure, appreciate that many changes can bemade in the specific embodiments which are disclosed and still obtain alike or similar result without departing from the spirit and scope ofthe invention.

1. Example 1 The Stability of Magnetic Microspheres Under PCR CyclingConditions

This study demonstrates the robust stability of the Luminex superparamagnetic microspheres in PCR cycling conditions. It alsodemonstrates that an amplicon can be captured and detected at variousstages of the PCR reaction as the concentration thereof increases. Thisstudy also shows that a two-probe system is a viable design forreal-time PCR detection using magnetic microspheres. Hybridizationprobes (US 2001/6174670) also use a two-probe system.

Experimental Design: A two probe system was used to detect thegeneration of a Factor V gene amplicon while in the presence of magneticmicrospheres that were coupled with target specific nucleotide probes. Atarget specific probe (FV Probe Ano) was attached to bead set 22. Thisprobe was not fluorescently labeled. Another probe was included in themix, which was not attached to a bead set, but was target specific, andlabeled with a Cy3 fluorophore on the 3′ end. A second bead (bead set27), coupled to an oligonucleotide sequence that is not specific to thetarget, was also added as a negative control.

A PCR cocktail was prepared using the following reagents andconcentrations:

1X (Invitrogen) 10X Buffer 5 μl (Invitrogen) dNTP (10 mM) 1 μl(Invitrogen) MgCl₂ (50 mM) 8 μl (IDT DNA) Primer 1 μl UCLA #25 Genomictemplate 1 μl (Invitrogen) Platinum Taq 0.4 μl (IDT DNA) Probe B 0.66 μl13-60022 Bead 22 3 μl 13-60027 Bead 27 3 μl Ambion H₂O 27.6 μl

Primers were used in optimized asymmetric concentrations, wherein theprimer amplifying the target sequence (FV Rev) was in a finalconcentration of 400 nM compared with the forward primer (FV Fwd52),which was in a final concentration of 50 nM in the PCR cocktail. Theconcentration of magnesium chloride in this reaction was optimized at ahigher concentration than normally would be expected from those skilledin the art. Because a heatable detection chamber was not available, aproof-of-concept experiment was set up such that the PCR cocktail wasmade, excluding genomic template. The cocktail was aliquoted into 16equal volumes of 48 μL each. Genomic template was added to each of thesealiquots and they were removed from the Perkin Elmer 9700 thermal cyclerat different cycle numbers of the PCR reaction. Immediately uponremoving the aliquots from the thermal cycler, and without any furtherreagent additions to the individual reactions, the aliquots were placedon a separate heater at 95° C. for 30 seconds and then at 52° C. for 3minutes. The aliquots were then immediately analyzed on a Luminex 100instrument without any further modifications. Both Luminex Magplexmicrosphere sets added were in a concentration of approximately 5000microspheres per reaction.

The cycling conditions for this reaction were as follows:

Heat Denaturation Step; 95° C. for 5 min.

Cycling Steps (for 43 cycles): 95° C. for 30 s, 45° C. for 45 s, 72° C.for 45 s.

The oligonucleotide sequences used in this study were ordered from IDTand are as follows:

Primers: FY Rev: (SEQ ID NO: 1) TGTTATCACACTGGTGCTAAAAAGG FY Fwd 52:(SEQ ID NO: 2) ACTACAGTGACGTGG Probes: Probe B short: (SEQ ID NO: 3)/3Cy3sp/ATAATGGGGCATTTCCTTCAAGAGAACAGTA FY Probe Ano: (SEQ ID NO: 4)/5AmMC12/TCTGGCTAGAACATGTTAGGTCTCCTGGCT/3InvdT/ AT-29: (SEQ ID NO: 5)/5AmMC12/AAAGAAAGGATTTGTAGTAAGATT

The Factor V Leiden genomic gene sequence (gi:2769646 and gi:488109) isshown in FIG. 13.

The data in Table 1 shows an increase in signal as the number of cyclesin the PCR reaction increases. The data shows an increase in signal forthe specific bead set (22), and no significant increase in signal forthe non-specific bead set (27). The signal here is shown as MedianFluorescent Intensity (MFI) from the Luminex Analyzer. This MFI wasobtained by measuring the reporter signal from approximately 100individually coupled magnetic beads and calculating the median.

TABLE 1 MFI for MFI for Cycle # Bead 22 Bead 27 0 5 5.5 3 7 4 6 13 8 910 10.5 12 11 8 15 7 3 18 11 11.5 21 19 8 24 27 15.5 27 35.5 12 30 45 1133 48.5 8 36 47 13.5 39 47 16.5 43 47 14 43 49 11.5

The data in Table 1 is graphically represented in FIG. 14. As can beseen in FIG. 14, the shape of the curve from bead set 22 is the shapethat one would expect from a typical real-time PCR reaction. This curvedisplays the baseline, the exponential, and the plateau phasesindicative of a PCR reaction.

Beads were coupled to capture probes using the following protocol:

1. Bring a fresh aliquot of −20° C., desiccated Pierce EDC powder toroom temperature.

2. Resuspend the amine-substituted oligonucleotide (“probe” or “capture”oligo) to 1 mM (1 nanomole/μL) in dH₂O.

3. Resuspend the stock uncoupled Luminex microspheres according to theinstructions described in the Product Information Sheet provided withthe microspheres.

4. Transfer 5.0×10⁶ of the stock microspheres to a USA Scientificmicrocentrifuge tube.

5. Pellet the stock microspheres by microcentrifugation at ≧8000×g for1-2 minutes.

6. Remove the supernatant and resuspend the pelleted microspheres in 50μL of 0.1 M MES, pH 4.5 by vortex and sonication for approximately 20seconds.

7. Prepare a 1:10 dilution of the 1 mM capture oligo in dH₂O (0.1nanomole/μL).

8. Add 2 μL (0.2 nanomole) of the 1:10 diluted capture oligo to theresuspended microspheres and mix by vortex.

9. Prepare a fresh solution of 10 mg/mL EDC in dH₂O. (Note: Return theEDC powder to desiccant to re-use for the second EDC addition.)

10. One by one for each coupling reaction, add 2.5 μL of fresh 10 mg/mLEDC to the microspheres (25 μg or ≅[0.5 μg/μL]_(final)) and mix byvortex.

11. Incubate for 30 minutes at room temperature in the dark.

12. Prepare a second fresh solution of 10 mg/mL EDC in dH₂O. (Note: Thealiquot of EDC powder should now be discarded.)

13. One by one for each coupling reaction, add 2.5 μL of fresh 10 mg/mLEDC to the microspheres and mix by vortex.

14. Incubate for 30 minutes at room temperature in the dark.

15. Add 1.0 mL of 0.02% Tween-20 to the coupled microspheres.

16. Pellet the coupled microspheres by microcentrifugation at ≧8000×gfor 1-2 minutes.

17. Remove the supernatant and resuspend the coupled microspheres in 1.0mL of 0.1% SDS by vortex.

18. Pellet the coupled microspheres by microcentrifugation at ≧8000×gfor 1-2 minutes.

19. Remove the supernatant and resuspend the coupled microspheres in 100μL of TE, pH 8.0 by vortex and sonication for approximately 20 seconds.

20. Enumerate the coupled microspheres by hemacytometer:

-   -   a. Dilute the resuspended, coupled microspheres 1:100 in dH₂O.    -   b. Mix thoroughly by vortex.    -   c. Transfer 10 μL to the hemacytometer.    -   d. Count the microspheres within the 4 large corners of the        hemacytometer grid.    -   e. Microspheres/μL=(Sum of microspheres in 4 large        corners)×2.5×100 (dilution factor).    -   f. Note: maximum is 50,000 microspheres/μL.

21. Store coupled microspheres refrigerated at 2-8° C. in the dark.

2. Example 2 Amplification Detection Using Tagged Primers

The following example demonstrates that a nucleic acid amplificationsignal can be measured in real-time using the tagged primer method. Thisexample also demonstrates that these measurements can be performed usinga imaging system comprising a quartz imaging chamber and a magnet thatcan be moved adjacent to the quartz imaging chamber to magnetically pullthe superparamagnetic particles to a two dimensional surface of thechamber opposite a charge coupled device (CCD) detector (see e.g., FIGS.1 and 2) in the presence of, and without modification to, the PolymeraseChain Reaction solution, and that the measurements thereof arecomparable to the Luminex 200 system. The imaging system comprising thequartz chamber and magnet may be considered a “static” imaging systemsince the detector takes an image of the particles and any moleculesbound to them while they are immobilized on the surface of the chamberby the magnetic field. In contrast, the Luminex 200 system may beconsidered a “flow” system since the particles are not immobilizedduring detection.

Experimental Design:

In this design, two primers were used, wherein one of the primers wasmodified with a Cy3 fluorophore at its 5′ end. The other primer wasmodified with a Carbon 18 spacer positioned between the target specificregion and a tag sequence complimentary to a specific probe (anti-tag)sequence attached to a superparamagnetic microsphere. In this case theprimer LUA-MEU had a tag sequence on the 5′ side of the C18 spacer(iSp18-IDT) that was complimentary to the Bead ME tf probe sequence thatwas coupled to bead set 43. In this study the primer sets were designedto amplify a region of the MTHFR Exon 7 gene sequence. Two LuminexMagPlex microsphere sets (Bead sets) were included in the PCR cocktail,during the PCR reaction. The probe attached to Bead set 43 wascomplementary to the 5′ tag sequence on the primer LUA-MEU-TF, whereasthe probe coupled to Bead set 12 was not complementary to the tagsequence of the primer in this reaction and thus served as a negativecontrol. Both Luminex Magplex microsphere sets added were in aconcentration of approximately 5000 microspheres per reaction.

A PCR cocktail was prepared using the following concentrations andreagents:

1x vol. μL Master Mix 25 HotStar TAQ Plus Master Mix 2X, Qiagen H₂O 21RNASE FREE Water, Qiagen Primer 1 IDT Template 1 Purified Human DNASample from UCLA Beads 2 Luminex Magplex microspheres total 50

The cycling conditions for this reaction were as follows:

Heat Denaturation Step; 95° C. for 5 min.

Cycling Steps (for 36 cycles): 94° C. for 30 s, 55° C. for 30 s, 72° C.for 30 s.

The oligonucleotide sequences used in this experiment were ordered fromIDT and were as follows:

Primers: LUA-MEU-TF: (SEQ ID NO: 16)CAAACAAACATTCAAATATCAATC/iSp18/CAAGGAGGAGCTGCTGAAG ATG LUA-MED-TF: (SEQID NO: 17) /5Cy3/CACTTTGTGACCATTCCGGTTTG Probes: Bead Set 43: Bead MEtf: (SEQ ID NO: 18) /5AmMC12/GATTGATATTTGAATGTTTGTTTG Bead Set 12:W12822: (SEQ ID NO: 19) /5AmMC12/ CAA CAG TGG AGG AAA GCC/3InvdT/Target sequence:

MTHFR Exon 7 (MRE7) [gi: 17444393] 112 bp (SEQ ID NO: 20)

In this experiment the primer concentrations and Magnesium Chlorideconcentrations did not need to be optimized. This was due to the natureof the design of the amplification primers wherein the amplified productcontains a single stranded overhang corresponding to the tag sequence.The C18 spacer blocks extension by the polymerase, such that the tagsequence complimentary to the probe on bead set 43 cannot serve as atemplate for second strand synthesis. Accordingly, the single strandedtag sequence on the 5′ end of the amplification product was able tohybridize to the probe without competition from a reverse complimentarystrand as occurs in the direct hybridization model.

In this study a PCR cocktail was made without template to be more thanenough volume to be aliquoted into 32 separate PCR tubes at a volume of50 uL each. This PCR cocktail included the two sets of Luminex MagPlexmicrospheres. Once mixed and aliquoted, 16 of the PCR reactions weremixed with genomic DNA, and 16 tubes were kept as no template (nt)reactions to serve as negative PCR controls. 8 positive samples and 8negative samples were analyzed using the Luminex LX200 instrument.Additionally, 8 positive and 8 negative samples were analyzed using the“static” imaging instrument described above. In each case of a set of 8samples, each sample was removed from the thermal cycler at variousstages of the PCR reaction. These samples were removed from the thermalcycler at the following cycles: 0, 5, 10, 15, 20, 25, 30, 35. Thereactions were stored temporarily at room temperature in the dark untilthe thermal cycling was completed.

Then the samples were placed on a 95° C. heater for 1 minute followed by10 minutes at 37° C.

These samples were also run on a Reliant Gel System Gel Cat. No. 54929to check for amplification specificity.

Data obtained from the “static” imaging instrument are included in Table2:

TABLE 2 Bead Regions 43 12 43 12 RP1 RP1 Count Count Median Median WellCycles No Template 111 177 234 232 A-1 0 Reactions 196 130 239 237 B-1 5150 109 229 225 C-1 10 177 135 233 235 D-1 15 194 123 248 248 E-1 20 181128 251 246 F-1 25 207 125 245 250 G-1 30 161 129 254 253 H-1 35 Genomic201 115 241 239 A-2 0 DNA added 160 112 242 239 B-2 5 173 117 245 245C-2 10 162 89 244 242 D-2 15 164 114 241 242 E-2 20 175 138 246 243 F-225 199 124 265 228 G-2 30 167 118 306 223 H-2 35

For the “static” imaging instrument, each sample was dispensed into thequartz imaging chamber and the encoded magnetic beads were pulled to theback of the chamber and held in place during analysis. This datadisplays the representative median values from the reporter wavelengths.Both bead sets were able to classify using the classificationwavelengths without any problem. Notice the increase in signal at cycles30 and 35 from bead set 43. This increase in signal is correlative tothe gel data with regard to amplification size and intensity.

Data obtained from the Luminex 200 Instrument (Table 3) using anidentical sample set up as the samples that were analyzed on the“static” imaging instrument (Table 2).

TABLE 3 Data Type: Median Bead 12 Bead 43 Total Location Cycles medianmedian Events No Template 1 (1, A1) 0 5 4 253 Reactions 2 (1, B1) 5 06.5 230 3 (1, C1) 10 3.5 6 243 4 (1, D1) 15 5 3.5 212 5 (1, E1) 20 3 4233 6 (1, F1) 25 0 2 245 7 (1, G1) 30 5.5 8 261 8 (1, H1) 35 4.5 0 268Genomic 9 (1, A2) 0 4 4.5 240 DNA added 10 (1, B2) 5 4.5 4 239 11 (1,C2) 10 5 5 218 12 (1, D2) 15 6.5 7 217 13 (1, E2) 20 4.5 0 239 14 (1,F2) 25 6.5 7 228 15 (1, G2) 30 0.5 26 232 16 (1, H2) 35 4 51 224

The data correlated with the data from the gel with regard toamplification size and intensity. A similar pattern of signal increasewas also shown using the “static” imaging system format.

3. Example 3 Multiplex of 8

In this example, the Direct Hybridization method was used with 8 primersets and 14 bead sets. An excess of bead sets were used to show that theamplification products do not non-specifically hybridize to bead setscontaining unrelated probes.

A PCR cocktail was made including the following reagents:

TABLE 4 1x vol. μL 45 Qiagen hotstart plus 2x Master 25 1125 Mix H₂OAmbion nuclease free H₂O 17 765 8 plex ordered from IDT Primer 1 45Coriell Sample 13033 Template 1 45 Luminex MagPlex Beads 3 135microspheres 50 mM mgCl₂ Qiagen 3 135 total 50 2250

This cocktail, including the Luminex MagPlex microspheres with probesequences attached thereto, was aliquoted into 40 PCR tubes at 50 μLeach. Then 20 of the reactions had approximately 100 ng of genomic DNAadded to them. These reactions were cycled on a BioRad iCycler thermalcycler. The primers were designed to amplify specific regions of thecystic fibrosis CFTR gene. Primer sequences for each of 8 primer setsused for this reaction are included in Table 5, including the finalconcentrations in each 50 μL reaction.

TABLE 5 Primer compositions Final Conc. Set name modification sequencescale bp purification (nM) 1 E20U None TTG AGA CTA CTG AAC ACT GAA GG100 23 desalt 75 (SEQ ID NO: 21) nmol 1 CE20D /5Cy3/ TTC TGG CTA AGT CCTTTT GC 100 20 HPLC 125 (SEQ ID NO: 22) nmol 2 E11U None TCA GAT TGA GCATAC TAA AAG TGA C 100 25 desalt 75 (SEQ ID NO: 23) nmol 2 CE11D /5Cy3/GAA CTA TAT TGT CTT TCT CTG CAA AC 100 26 HPLC 125 (SEQ ID NO: 24) nmol3 E11U2 None AAG TTT GCA GAG AAA GAC AAT ATA G 100 25 desalt 100 (SEQ IDNO: 25) nmol 3 CE11D2 /5Cy3/ GAA TGA CAT TTA CAG CAA ATG C 100 22 HPLC200 (SEQ ID NO: 26) nmol 4 E4U None TTT GTA GGA AGT CAC CAA AGC 100 21desalt 75 (SEQ ID NO: 27) nmol 4 CE4D /5Cy3/ GAG CAG TGT CCT CAC AAT AAAGAG 100 24 HPLC 125 (SEQ ID NO: 28) nmol 5 CE21U /5Cy3/ TGC TAT AGA AAGTAT TTA TTT TTT CTG G 100 28 HPLC 125 (SEQ ID NO: 29) nmol 5 E21D NoneAGC CTT ACC TCA TCT GCA AC 100 20 desalt 75 (SEQ ID NO: 30) nmol 6 CE7U/5Cy3/ GAA CAG AAC TGA AAC TGA CTC G 100 22 HPLC 200 (SEQ ID NO: 31)nmol 6 E7D3 None CAG GGA AAT TGC CGA GTG 100 18 desalt 100 (SEQ ID NO:32) nmol 7 CC7U /5Cy3/ GAC TTG TCA TCT TGA TTT CTG G 100 22 HPLC 125(SEQ ID NO: 33) nmol 7 C7D None TTT GGT GCT AGC TGT AAT TGC 100 21desalt 75 (SEQ ID NO: 34) nmol 8 BE9U /5Cy3/ TCA CTT CTT GGT ACT CCT GTCC 100 22 HPLC 125 (SEQ ID NO: 35) nmol 8 E9D None CAA AAG AAC TAC CTTGCC TGC 100 21 desalt 75 (SEQ ID NO: 36) nmol

The cycling conditions for this reaction were as follows:

Heat Denaturation Step: 95° C. for 10 min.

Cycling Steps (for 36 cycles): 94° C. for 30 s, 56° C. for 90 s, 72° C.for 90 s.

Individual PCR samples were removed at various cycles during the PCRreaction. These tubes were removed during the 56° C. step at theirrespective cycle numbers. Both “no template” and “template positive”samples were removed simultaneously at the following cycle numbers: 5,8, 12, 16, 20, 24, 28, 30, 36, and 36 again. These samples that werepulled off the thermal cycler were stored in the dark at roomtemperature until the completion of all 36 cycles. Without any furthermodifications to the samples regarding addition of reagents, thesesamples were heated to 95° C. for 1 minute, and then incubated at 44° C.for 15 minutes and then analyzed on a Luminex 200 instrument and on a“static” imaging system as described above. Although a heatabledetection chamber was not available at the time, the design of thisexperiment shows that it is possible to perform this reaction inreal-time, if the general procedures described herein are adapted toanalysis in a detection chamber capable of thermal cycling.

The bead sets used in the reactions and the probes that were coupled tothem are contained in Table 6.

TABLE 6 Target Bead Primer Set name modification sequence scale bppurification Set 12 W12822 /5AmMC12/ CAA CAG TGG AGG AAA GCC 100 nmol 18desalt /3InvdT/ (SEQ ID NO: 37) 19 G1717 /5AmMC12/ TTG GTA ATA GGA CATCTC CA 100 nmol 20 desalt 2 /3InvdT/ (SEQ ID NO: 38) 18 R560 /5AmMC12/CTT TAG CAA GGT GAA TAA CT 100 nmol 20 desalt 3 /3InvdT/ (SEQ ID NO: 39)20 R117 /5AmMC12/ AGG AGG AAC GCT CTA TCG CG 100 nmol 20 desalt 4/3InvdT/ (SEQ ID NO: 40) 22 N1303 /5AmMC12/ GGG ATC CAA GTT TTT TCT AA100 nmol 20 desalt 5 /3InvdT/ (SEQ ID NO: 41) 25 1078T2 /5AmMC12/ CACCAC AAA GAA CCC TGA 100 nmol 18 desalt 6 /3InvdT/ (SEQ ID NO: 42) 36A455 /5AmMC12/ CCA GCA ACC GCC AAC AAC TG 100 nmol 20 desalt 8 /3InvdT/(SEQ ID NO: 43) 38 3659C2 /5AmMC12/ TTG ACT TOG TAG GTT TAC 100 nmol 18desalt none /3InvdT/ (SEQ ID NO: 44) 35 G278952 /5AmMC12/ TGG AAA GTGAGT ATT CCA TGT C 100 nmol 22 desalt none /3InvdT/ (SEQ ID NO: 45) 372184A7 /5AmMC12/ GAA ACA AAA AAA CAA TC 100 nmol 17 desalt none /3InvdT/(SEQ ID NO: 46) 39 G18982 /5AmMC12/ TAT TTG AAA GGT ATG TTC TTT G 100nmol 22 desalt none /3InvdT/ (SEQ ID NO: 47) 42 G31202 /5AmMC12/ CTT CATCCA GGT ATG TAA AAA T 100 nmol 22 desalt none /3InvdT/ (SEQ ID NO: 48)44 G85 /5AmMC12/ ATT TGA TGA AGT ATG TAC CTA T 100 nmol 22 desalt none/3InvdT/ (SEQ ID NO: 49) 43 C3849 /5AmMC12/ GTC TTA CTC GCC ATT TTA AT100 nmol 20 desalt 7 /3InvdT/ (SEQ ID NO: 50)

The Cystic Fibrosis gene sequences (SEQ ID NO: 8-15) used in thisexperiment are given in FIG. 15. The results from the reaction wereconfirmed by analysis on a gel.

Data was collected using a Luminex 200 instrument, while at 44° C. Datacollected is represented in Table 7. All template positive samples whosevalues are distinguishable from the noise are shaded in Table 7. Furtheroptimization techniques known to those skilled in the art may be used tomodify the reaction conditions and further improve the signal-to-noiseratio. The bead sets whose MFI values were expected to be targetspecific to the amplicon rose above the noise toward the latter end ofthe reaction. The bead sets whose probes were expected to benon-specific or negative did not.

TABLE 7

Data was collected using the “static” imaging system, while at 44° C.Net data collected using the “static” imaging system is represented inTable 8. All positive samples whose values are distinguishable from thenoise are highlighted in Table 8. The raw data from the “static” imagingsystem that was used to create Table 8 is represented in Table 9. Table8 was calculated by taking the average MFI from data points of all beadssets with template negative samples for all cycles and subtracting thataverage from all data points. In the case where the resulting sum ofthat calculation was negative, all negative numbers were converted tozero. Some of the lower cycle numbers contained spurious results, whichcan be considered outliers.

TABLE 8

The raw data from the “static” imaging system that was used to createTable 8 is represented in Table 9.

TABLE 9

***

All of the compositions and methods disclosed and claimed herein can bemade and executed without undue experimentation in light of the presentdisclosure. While the compositions and methods of this invention havebeen described in terms of certain embodiments, it will be apparent tothose of skill in the art that variations may be applied to thecompositions and methods and in the steps or in the sequence of steps ofthe methods described herein without departing from the concept, spiritand scope of the invention. More specifically, it will be apparent thatcertain agents which are both chemically and physiologically related maybe substituted for the agents described herein while the same or similarresults would be achieved. All such similar substitutes andmodifications apparent to those skilled in the art are deemed to bewithin the spirit, scope and concept of the invention as defined by theappended claims.

REFERENCES

The following references, to the extent that they provide exemplaryprocedural or other details supplementary to those set forth herein, arespecifically incorporated herein by reference.

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1. A method of amplifying and detecting a plurality of nucleic acidtargets in a sample comprising: (a) combining in a chamber a samplecomprising the plurality of nucleic acid targets, a plurality of primerpairs for priming amplification of the plurality of nucleic acidtargets, a labeling agent, and a first plurality of probes complementaryto the plurality of nucleic acid targets, wherein the probes areimmobilized on a plurality of encoded magnetic beads such that theidentity of each probe is known from the encoded magnetic bead on whichit is immobilized; (b) performing an amplification cycle to form labeledamplification products for each of the plurality of nucleic acid targetsamplified with the plurality of primer pairs; (c) hybridizing thelabeled amplification products to the probes immobilized on the encodedmagnetic beads; (d) applying a magnetic field to a surface of thechamber to draw the encoded magnetic beads and the labeled amplificationproducts hybridized to the probes immobilized on the encoded magneticbeads to the surface of the chamber; (e) detecting a signal from theencoded magnetic beads and a signal from the labeled amplificationproducts; (f) removing the magnetic field from the surface of thechamber prior to performing a further amplification cycle; and (g)repeating steps (b) through (f) at least once; wherein the plurality ofnucleic acid targets in the sample are amplified and detected.
 2. Themethod of claim 1, further comprising correlating the signal from thelabeled amplification product with the concentration of the nucleic acidtarget in the sample.
 3. The method of claim 1, wherein the plurality ofprimer pairs is further defined as between 8 to 500 distinct primerpairs.
 4. The method of claim 1, wherein the labeling agent is attachedto one primer of each of the primer pairs.
 5. The method of claim 1,wherein the chamber is a quartz chamber.
 6. The method of claim 1,wherein the labeling agent is a fluorescent dye.
 7. The method of claim1, wherein the labeling agent is a fluorescence resonance energytransfer pair.
 8. The method of claim 1, further comprising combining inthe chamber a second plurality of probes complementary to the pluralityof nucleic acid targets, wherein the second plurality of probes are notimmobilized on the plurality of encoded magnetic beads and furtherwherein the second plurality of probes are complementary to differentregions on the plurality of nucleic acid targets than the firstplurality of probes.
 9. The method of claim 8, wherein one member of afluorescence resonance energy transfer pair is attached to the firstplurality of probes immobilized on the encoded magnetic beads and theother member of the fluorescence resonance energy transfer pair isattached to the second plurality of probes that are not immobilized onthe encoded magnetic beads.
 10. The method of claim 1, wherein thelabeling agent is a fluorophore and quencher pair.
 11. The method ofclaim 1, wherein the labeling agent is a DNA intercalating agent. 12.The method of claim 1, wherein the encoded magnetic beads are encodedwith fluorescent dyes.
 13. The method of claim 12, wherein the encodedmagnetic beads are encoded with different fluorescent intensities. 14.The method of claim 12, wherein the encoded magnetic beads are encodedwith different fluorescent emission wavelengths.
 15. The method of claim1, wherein the encoded magnetic beads are superparamagnetic.
 16. Themethod of claim 1, wherein applying the magnetic field comprises placinga permanent magnet adjacent to the surface of the chamber.
 17. Themethod of claim 1, wherein applying the magnetic field comprises turningon an electromagnet adjacent to the surface of the chamber.
 18. Themethod of claim 1, wherein the magnetic field is applied during a primerannealing phase of the amplification cycle.
 19. The method of claim 1,wherein the magnetic field is applied during a primer extension phase ofthe amplification cycle.
 20. The method of claim 1, wherein the magneticfield is applied following the amplification cycle.
 21. The method ofclaim 1, wherein detecting the encoded magnetic beads and the labeledamplification products comprises imaging fluorescent wavelengths emittedfrom the encoded magnetic beads and the labeled amplification products.22. The method of claim 1, wherein removing the magnetic field comprisesremoving a permanent magnet from a position adjacent to the surface ofthe chamber.
 23. The method of claim 1, wherein removing the magneticfield comprises turning off an electromagnet adjacent to the surface ofthe chamber.
 24. The method of claim 1, wherein steps (b) through (f)are repeated between 10 to 40 times.
 25. The method of claim 1, whereinthe plurality of probes comprise a blocked 3′ hydroxyl group.
 26. Themethod of claim 25, wherein the 3′ hydroxyl group is blocked with aphosphate group.
 27. The method of claim 25, wherein the 3′ hydroxylgroup is blocked with a 3′ inverted dT.
 28. A method of amplifying anddetecting a plurality of nucleic acid targets in a sample comprising:(a) combining in a chamber a sample comprising the plurality of nucleicacid targets, a plurality of primer pairs for priming amplification ofthe plurality of nucleic acid targets, and a plurality of molecularbeacons complementary to the plurality of nucleic acid targets, whereinthe molecular beacons are immobilized on a plurality of encoded magneticbeads such that the identity of each molecular beacon is known from theencoded magnetic bead on which it is immobilized; (b) performing anamplification cycle to form amplification products for each of theplurality of nucleic acid targets amplified with the plurality of primerpairs; (c) hybridizing the amplification products to the molecularbeacons immobilized on the encoded magnetic beads; (d) applying amagnetic field to a surface of the chamber to draw the encoded magneticbeads and the amplification products hybridized to the molecular beaconsimmobilized on the encoded magnetic beads to the surface of the chamber;(e) detecting a signal from the encoded magnetic beads and a signal fromthe molecular beacons; (f) removing the magnetic field from the surfaceof the chamber prior to performing a further amplification cycle; and(g) repeating steps (b) through (f) at least once; wherein the pluralityof nucleic acid targets in the sample are amplified and detected.
 29. Amethod of amplifying and detecting a nucleic acid target in a samplecomprising: (a) combining in a chamber a sample comprising the nucleicacid target, a primer pair for priming amplification of the nucleic acidtarget, and a probe set complementary to the nucleic acid target,wherein the probe set comprises a first probe immobilized on a magneticbead, and a second probe comprising a label; (b) performing anamplification cycle to form amplification products for the nucleic acidtarget amplified with the primer pair; (c) hybridizing the amplificationproducts to the probe set; (d) applying a magnetic field to a surface ofthe chamber to draw the magnetic bead and the amplification productshybridized to the probe immobilized on the encoded magnetic bead to thesurface of the chamber; (e) detecting a signal from the second probehybridized to the amplification products; (f) removing the magneticfield from the surface of the chamber prior to performing a furtheramplification cycle; and (g) repeating steps (b) through (f) at leastonce; wherein the nucleic acid target in the sample is amplified anddetected.
 30. The method of claim 29, wherein the magnetic bead is anencoded magnetic bead.
 31. The method of claim 29, further defined as amethod of amplifying and detecting a plurality of nucleic acid targetscomprising: (a) combining in the chamber a sample comprising a pluralityof nucleic acid targets, a plurality of primer pairs for primingamplification of the plurality of nucleic acid targets, and a pluralityof probe sets complementary to the plurality of nucleic acid targets,wherein each probe set comprises a first probe immobilized on an encodedmagnetic bead such that the identity of the first probe is known fromthe encoded magnetic bead on which it is immobilized, and a second probecomprising a label; (b) performing an amplification cycle to formamplification products for each of the plurality of nucleic acid targetsamplified with the plurality of primer pairs; (c) hybridizing theamplification products to the probe sets; (d) applying a magnetic fieldto a surface of the chamber to draw the encoded magnetic beads and theamplification products hybridized to the probes immobilized on theencoded magnetic beads to the surface of the chamber; (e) detecting asignal from the encoded magnetic beads and a signal from the secondprobe hybridized to the amplification products; (f) removing themagnetic field from the surface of the chamber prior to performing afurther amplification cycle; and (g) repeating steps (b) through (f) atleast once; wherein the plurality of nucleic acid targets in the sampleare amplified and detected.
 32. A method of amplifying and detecting anucleic acid target in a sample comprising: (a) combining in a chamber asample comprising the nucleic acid target, a primer pair for primingamplification of the nucleic acid target, a dNTP coupled to a quenchermolecule, and a fluorescently labeled probe complementary to the nucleicacid target, wherein the probe is immobilized on a magnetic beads; (b)performing an amplification cycle to form amplification products of thenucleic acid target, the amplification products comprising quenchermolecules; (c) hybridizing the amplification products to the probeimmobilized on the magnetic bead; (d) applying a magnetic field to asurface of the chamber to draw the magnetic bead and the amplificationproducts hybridized to the probe immobilized on the encoded magneticbead to the surface of the chamber; (e) detecting a signal from thelabeled probe, wherein a decrease in the signal from the labeled probeindicates hybridization of the labeled probe to the amplificationproducts comprising quencher molecules; (f) removing the magnetic fieldfrom the surface of the chamber prior to performing a furtheramplification cycle; and (g) repeating steps (b) through (f) at leastonce; wherein the nucleic acid target in the sample is amplified anddetected.
 33. The method of claim 32, wherein the magnetic bead is anencoded magnetic bead.
 34. The method of claim 32, further defined as amethod of amplifying and detecting a plurality of nucleic acid targetscomprising: (a) combining in the chamber a sample comprising theplurality of nucleic acid targets, a plurality of primer pairs forpriming amplification of the plurality of nucleic acid targets, a dNTPcoupled to a quencher molecule, and a plurality of fluorescently labeledprobes complementary to the plurality of nucleic acid targets, whereinthe probes are immobilized on a plurality of encoded magnetic beads suchthat the identity of each probe is known from the encoded magnetic beadon which it is immobilized; (b) performing an amplification cycle toform amplification products comprising quencher molecules for each ofthe plurality of nucleic acid targets amplified with the plurality ofprimer pairs; (c) hybridizing the amplification products to the probesimmobilized on the encoded magnetic beads; (d) applying a magnetic fieldto a surface of the chamber to draw the encoded magnetic beads and theamplification products hybridized to the probes immobilized on theencoded magnetic beads to the surface of the chamber; (e) detecting asignal from the encoded magnetic beads and a signal from the labeledprobes, wherein a decrease in the signal from the labeled probesindicates hybridization of the labeled probes to the amplificationproducts comprising quencher molecules; (f) removing the magnetic fieldfrom the surface of the chamber prior to performing a furtheramplification cycle; and (g) repeating steps (b) through (f) at leastonce; wherein the plurality of nucleic acid targets in the sample areamplified and detected.
 35. A method of amplifying and detecting aplurality of nucleic acid targets in a sample comprising: (a) combiningin a chamber a sample comprising the plurality of nucleic acid targets;a plurality of primer pairs for priming amplification of the pluralityof nucleic acid targets, wherein each primer pair comprises a firstprimer comprising a target specific sequence, a tag sequence 5′ of thetarget specific sequence, and a blocker between the target specificsequence and the tag sequence, and a second primer comprising a targetspecific sequence; a labeling agent; and a plurality of probescomplementary to the tag sequences of the plurality of primer pairs,wherein the probes are immobilized on a plurality of encoded magneticbeads such that the identity of each probe is known from the encodedmagnetic bead on which it is immobilized; (b) performing anamplification cycle to form tagged and labeled amplification productsfor each of the plurality of nucleic acid targets amplified with theplurality of primer pairs; (c) hybridizing the tagged and labeledamplification products to the probes immobilized on the encoded magneticbeads; (d) applying a magnetic field to a surface of the chamber to drawthe encoded magnetic beads and the tagged and labeled amplificationproducts hybridized to the probes immobilized on the encoded magneticbeads to the surface of the chamber; (e) detecting the encoded magneticbeads and the tagged and labeled amplification products; (f) removingthe magnetic field from the surface of the chamber prior to performing afurther amplification cycle; and (g) repeating steps (b) through (f) atleast once; wherein the plurality of nucleic acid targets in the sampleare amplified and detected.
 36. The method of claim 35, wherein thelabeling agent is a reporter molecule attached to the second primer ofthe primer pair.
 37. The method of claim 35, wherein the labeling agentis an intercalating dye.